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For tagging files: Leap http://www.yepsoftware.com/leap/index.html DEVONthink Has import files and folders option, tag support and you get advanced search (boolean etc.) as well http://www.devon-technologies.com/products/devonthink/devonthink2.html

If your professor uses a Mac, consider Devonthink by DevonTechnologies.
http://www.devon-technologies.com/products/devonthink/index.html

For searching, the software has an artificial intelligence system, keywords, meta data. It can store PDFs, word docs, emails, notes. It can be integrated with a scanner so you can scan and store documents in the database. It's got OCR built in...

I have DevonThink (personal edition, not Pro/Office) and I don't even use 1/10 of the power built into this system. You should check out some of the reviews online and videos of people using DevonThink.

http://www.devon-technologies.com/products/devonagent/index.html Devon-Technologies makes some great software also for finding and researching information, still doesn't provide much more then relevancy though. No real evaluation methodology, this is mainly left to your own critical thinking capacity. Unfortunately this "capacity" is often times ignored in terms of most education systems, and at best possibly overlooked or students may even be given a dash of critical thinking knowledge. Although they really need this more then anything. Research databases from your university libraries, etc. are obviously some of the best places to look as these libraries pay large sums of currency to allow students access. They are generally not paying for garbage articles written by morons, I have a slight bit more faith in their selection capacity. I think that's safe to hope for at least.

And what the hell does "potential software base" mean? I have no idea, but I do know that lots of Mac applications exist. That doesn't even count some of the big ones, like those produced by Omni or something like Delicious Library and DEVONtechnologies.

http://www.devon-technologies.com/products/devonth ink/

Using a good PDF exporter (I'm on OS X, so look elsewhere for free & easy ways to do this on Windows), DEVONthink will pretty much keep everything organized like a digital filing cabinet.

'Course, the cheapest version costs $39.95, but I can attest to the fact that this software WORKS (I got it heavily discounted in the MacHeist 2006 bundle).

Linked version with condensed summary. I wanted to find out more about some of them. Others may benefit too.

Ecto a blogging client (but the site seems to be down: try this for more info). Shareware, $17.95.
Transmit an FTP client. Shareware, $17.95
Sync Services -- comes with 10.4
BBedit text/html editor. $125, but worth it.
Missing Synch for Windows Mobile - synchronize with PDA/smartphones. $49.95/$39.95
OmniGraffle - diagramming / flowchart program. $79.95 / $149.95
ConceptDraw - another diagramming / flowchart program. $299
IChat AV - built-in to 10.4
AppleScript, Scriptdebugger - also built-in. No link. I'm getting lazy.
Microsoft Entourage -- part of MS Office.
Sketchfigher 4000 Alpha -- a game from the great Ambrosia Software. $19.00
TypeIt4Me - keyboard macro expander. $27
NetworkLocation - automatically trigger configuration changes depending upon where you are on the network (e.g., at home, work, etc.). $15
Apple Remote Desktop 3 - control / configure Mac systems remotely. $499 / $299 (unlimited / 10 systems)
MacLinkPlus - file conversion software (e.g., from WordPerfect documents to/from Word, and many others). $79
Parallels Desktop for Mac - virtualization software (e.g., run Win XP simultaneously with OS X). $79.
Remote Desktop Connection - connect remotely to a Windows desktop. FREE
Snap X Pro - screen / movie capture. $29
Boot Camp - dual boot Windows. I'm lazy.
PDF - Portable Document Format from Adobe? What?
Lingon - tool for making launchd scripts for 10.4.
Workgroup Manager - manage local systems - part of 10.4 Server.

---
Okay, a mildly interesting list. Here's a few more suggestions:

Cyberduck - FTP and SFTP client. Donationware.
VLC - cross-platform video viewer / transcoder.
Blender 3D - cross-platform 3D modelling / rendering.
Bookends - excellent bibliography software. $99
Celestia - cross-platform real-time 3D astronomy simulator.
Plot - a, uh, plotting / graphing program.
proFit - another plotting / graphing program, non-free. $95
WordService - adds a bunch of text reformatting tools to the Services menu, making them accessible in any program. The same page has a bunch of other useful and free services.

The original article lists PDF, but no tools. While its true OS X native support makes PDF pretty easy to use, there's still some tasks that are awkward and some useful tools out there to do t

I'm not familiar with OneNote, but I've heard it mentioned in discussions of outlining / note-taking / "junk drawer" apps., such as OmniOutliner, DEVONthink, and Yojimbo. This seems to be a particularly hot genre on the Mac right now.

I don't know what alternatives there are for other platforms, but DEVONagent has advanced search features, like boolean operations and plug-ins for various specialty search engines. It can also do deep-scanning searches (following links) and is good at filtering out junk. I find the NEAR operator is immensely useful for day-to-day searches, finding terms that are closely related - but rejecting terms that simply appear on the same page in different contexts, while not requiring them to be in an exact sequence like using quotes would.

Get EasyFind from http://www.devon-technologies.com/products/freewar e/applications.php. It works without Spotlight.

A laptop would enable me to do a number of things that a pen and paper wouldn't ( or wouldn't do as well):

I can enter my notes into an application like DEVONthink which not only allows me to keep rich notes with wiki-style linking, but also allows me to search my old notes, papers, etc. for similar content (or just some phrase/topic) and present me with the top matches in a snap. This is no more distracting than writing notes and drawing figures during class.

I can hook up a camera like an iSight (or other) to record portions (or all) of the lecture for review back in the dorms. This is less distracting than writing, as I only need to check the frame every now and again.

Ditto for audio recording.

I can have a window open with my OCaml/Lisp/whatever REPL open to try out concepts as the professor relays them. Looking at code on a board or screen doesn't help me understand it nearly as much as typing it and running it. Slightly more distracting than handwriting, but with a bigger payoff.

I can more efficiently annotate PDFs.

I can use an editor like SubEthaEdit to take notes in a collaborative manner with my classmates, possibly even having a backchannel discussion about the material without disrupting the class. Again, more distracting, but with a much higher payoff.

And of course, most importantly, I can watch porn.

DevonThink http://www.devon-technologies.com/ for OSX can display multiple file types (rtf, pdf, images, movies), and has very powerful classification functions (that's its main purpose). But it doesn't handle presentation formats, as far as I know.

2. The dock is cool and all, because 90% of the time I'm using the same dozen or so apps. But for those lesser-used programs the options are either clutter your dock, or have to open and sort through the app folder every time.

3. Closing the last window of a program doesn't terminate the program - quite different than other OS's - and it means I have to rember apple-Q instead of clicking the x to actually quit

Quite... I just want to say something:

I think that abandoning bookmarks altogether is a bad idea.

Search, while useful, only works if you can find the exact keywords necessary to bring up a certain page. Search merely complements, rather than replaces, bookmarks.

Looking through my bookmark lists, I see many websites which I would never have known how to search for (they're mostly websites I stumbled upon from other websites). Some of these sites are hard to find because:

1) they don't have enough Statistically Improbable Words. e.g. try searching for software that describes biology of a python.

2) the page doesn't contain words associated with its significance to me (yes, it can happen). e.g. let's say you come across a page that has a nice layout that you want to revisit later -- if you ever forget the keywords on that page, you may never find it again. Whereas if I were to file it under "Nice websites" in my bookmark folder, I'd be able to find it again.

3) I can't remember any of the keywords associated with the page.

4) I forget that I've ever visited those webpages. Some search engines (e.g. a9.com) have histories that you can revisit, but they're no use unless you can classify them. And if you classify them, they're basicallly bookmarks.

I think the reason people dislike bookmarks is because they're a hassle to organize. We need some sort of tool to autoorganize bookmarks.

There two basic requirements:
1) Multiple hierarchy - a bookmark must be able to belong to more than one category. Example of this is GMail's labels -- each email can belong to more than one label.

2) Automatic classification - the proper term for this is automatic taxonomy. This can be accomplished using a Bayesian algorithm (like the one POPmail is using). In fact, DEVONthink already does this.

When a user makes a bookmark, the program should come up with a list of category folders (sorted from likeliest to least likely) to file that bookmark under, and the user must be allowed to select more than one folder.

I'd love tgo switch to NeoOffice or Pages or another decednt alternative to Word on the OS X platform, but they all ignore a feature of vital importance to professional writers like myself: A halfway decent word count function.

Yeh, that's why I'm sticking with "vi". Being able to go ":,'aw !wc" or "!}fmt" or "!/^From/-1sort" instead of having to write a script or cut-and-paste from a whole other document is a killer feature.

OK, OK, I'm a retro old fogey. I won't tease you any more (but I really do prefer to work in "vi" than GUI apps)... but this isn't entirely irrelevant either... because Mac OS X has a really neat capability that many people don't fully "get", that gives you a lot of this kind of easy integration between applications that made UNIX such a revolutionary environment back in the '70s (and, goldarnit, still does today).

In Pages, you can do a word count on the whole document, but not on a highlighted selection.

Does the Services menu not work in Pages? I'm sure it does. In any Cocoa app and many Carbon ones you can select text and perform operations on it through "Application -> Services", and any application can publish a service in the Services menu. There's a freeware application called "WordService" that provides among other things a "statistics" dialog that gives you characters, spaces, words, and lines in the selected text.

I don't know how well NeoOffice/J supports services, but Pages is Apple's own application so I would be positively astounded if it fell short in this area. This kind of deep integration between applications is what really makes Mac OS X a joy for me. You don't need to provide every feature over and over again in every application, you just need to provide a way for programs to work together.

...NeoOffice or Pages or another decednt[sic] alternative to Word on the OS X platform, but they all ignore a feature of vital importance to professional writers like myself: A halfway decent word count function.

Actually, while the programmers of Pages may not "get it," because it is a native application and because the programmers of OS X do "get it," you can just install a system service that will perform a word count on a selection. In fact there is a set of services called "Wordservice" that is free and includes that functionality as well as many more (like: Reformat, Remove line attachments/endings/links/multiple spaces/multiple feeds/quotes, Trim line beginnings/line endings/lines, Sort lines ascending/descending, Shift left/right, Initial caps of words/sentences, All caps & lowercase, Mac/Windows/Unix line endings, Rotate 13, Straight/Smart Quotes, Encode/Decode tabs, Insert date/date & time/time/contents of path, Speak native/german text). You can download it from here. System services work on all cocoa applications like Word, Pages, Indesign, TextEdit, Safari, etc. They do not work on NeoOffice/J though, which is for me one of it's biggest failings.

...for now Word is the only real option for anyone who earns his or her living as a writer.

OK, now you've really confused me. You're a professional writer who uses Word? I'm so very sorry. For larger, technical works Latex or Framemaker are both much, much better options. They are actually designed to create and layout books, not memos. For writing non-technical works or if you don't need to do layout there are many text editors that don't have the bugs/limitations of word and provide very useful features.

I've worked at a place that used word for actual writing, but we had to give it up very quickly. Larger files (200+ pages with some embedded images) would regularly become corrupted and either fail to save, or save but fail to open. The layout features were incredibly weak and everyone was reduced to using carriage returns to try to place text and objects. I'll tell you right now, I have written professionally as all or a large part of my job for many years and Word is a non-starter.

• VoodooPad: An excellent WYSWIG Wiki-like notebook
  
• Circus Ponies NoteBook: A visually impressive note-taking app that looks like a real lab notebook.
  
• Hog Bay Notebook: Similar to the above, but lightweight and with IMHO superior outlining facilities.
  
• PersonalWiki : A desktop interface to the web-based ZWiki.
  
• Devonthink: A note/snippet/document management system, which includes semi-supervised classification algorithms.
  

"Content indexing is currently four to five times faster than the one of Panther, not limited to the first 100 KB of the documents, not case insensitive, does include all words and all numbers . . . DEVONthink is able to preview found documents (including highlighting of occurrences)."

Never mind that DT also shows you related items - love that AI - surfs the web, clips, composes, views images, does the dishes and turns out the lights.

Are you thinking Mac OS X uber-app? I am. I run my computer and my life thru DevonTech, including writing to web and for print.

With Launchbar (or Quicksilver) and any Devon app, you don' need no steekin' Spotlight.

If you have a mac and want a great search tool try DevonAgent:
http://www.devon-technologies.com/products/devonag ent/overview.php

Whoops... Anyway, I think they can be a definite selling point in that OS-level search capabilities integrate better into the user experience.

For one, OS integration gives you the ability to create "smart" (dynamic) folders which are basically the results of a query against metadata in all files but still have a system-level validity.

In other words, you can create your "Yosemite" folder which will contain anything related to that keyword, and you can do that with other programs, such as DevonTHINK. What you can't have with third-party apps (AFAIK) is automatic scanning of files across the entire system without prior settings, and most of all, the ability to treat "catalogs" as real directories which you can burn to CD, backup, compress & archive, etc...

More to the point, do these third-party apps offer APIs to other applications, so that you can use their functionality, say, when saving a file or including a picture from your library? That's what OS-level search capabilities are about, at least the way I understand them.

Alternatively, you could purchase DEVONAgent, which searches many engines, and then integrates the results, removing redundant, and/or unrelated links before presenting you with the results (ordered by relevancy).

No, it's not free, and yes, it's only for the Mac, but it's a good example of how many people are finding the information they need, without getting bogged down in this "My site ranks higher than yours" mentality, which seems to be permeating Google lately. Copernic for the PC used to be free, and did something similar (integrating multiple searches into one set of results), but it lacks the functionality which DEVONAgent brings to the table (and if you're impressed with the Agent app, you should check out DEVONthink - It's one of my fave Mac programs, and ranks right up their with Quicksilver and Delicious Library, as a must-have app!)

I agree with the original poster... Google's results pretty much suck lately. Around November of last year, I began to notice this. Nowadays, it takes much longer to find the needle in that haystack! The 2nd post in this thread is nice (add "-buy, etc"), but it doesn't help if you're actually looking for something to buy.

Download WordService here, And you can count the words in whatever text you're selecting (in any application), just by pressing shift-command-I, or selecting "Statistics..." from the services menu. Pretty handy.

I must confess to enjoying the feel of fresh pen on paper. And I have printed countless copies of nearly identical sections of writing, just so that my pen can run across the paper. Of course, when visceral pleasure runs out, practicality must take over, and it's easier to manage a large digital collection of scraps than a large pile of scrap paper. And so I have turned to DevonThink, a mac-only program that I am thrilled with. It makes it terrifically simple to edit many little scraps, and organize them into useful groupings. I will always relish the pen, but when work needs done, DevonThink does the trick.

Here's a link to a freeware app that already enables Cocoa applications to do a similar thing, but with text only: AntiWord Service. It works on Mac OS X 10.1.5 and higher.

well, one I've played with is:

DEVONthink

It's really cool and great for exactly what you describe: storing a bunch of loosely-connected information that you need to search and cluster into categories.

You just add your text and it will automatically classify it using semantic analysis.

But alas, it is for Mac only and is not Free.

If anybody knows about anything like this for Linux, and Free, I'd love to hear about it....