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I don't have a Kindle, but a simple google search results in this being among the first apps that will convert PDFs to Kindle, running on OS X and Linux, as well as Windows...
http://calibre.kovidgoyal.net/

Here's another page on constructing an ePub file. It's much easier than I thought, and the page has a nice set of template files. And the format is supported by Calibre, which is a great tool for converting between ebook formats.

The thing is, we should have been at this point a long time ago ... but noooooo. Every company had to try their own hairbrained proprietary scheme and hope they could get everyone else to conform to it and pay royalties, even though the basic idea is, well, kind of obvious these days (some kind of XTML/CSS-based format).

I suppose some patent troll will probably try to undermine ePub too.

How about a list of more apps?

• Calibre ebook manager
• Last.fm streaming music client
• VLC media player
• CDex CD ripping software
• MusicBrainz Picard for tagging audio files
• Pidgin IM client
• OpenPandora to put Pandora on your desktop and scrobble to Last.fm
• VirtualDub for simple video editing

Anyone else have any good recommendations?

Here. Doesn't work for .AZW1 or .TPZ files. And use Calibre to manage your collection.

Formats don't matter, so long as they're open. If you've got something that your reader can't handle, use Calibre to convert it to a format which can be handled, and that's it.

That said, I'm also using Sony (PRS-505 though, I prefer higher contrast and whiter background over the dubious convenience of a touch screen), and the online store that I buy books from can provide them directly in Sony's native LRF format (among other things). And no, it's not Sony's store, and there's no DRM.

I got the PRS-700 just after christmas and I love it. the Sony software on the other hand, is just like wow. Worst. Software. Ever. The Sony softwawas uninstalled on day 2 of my ownership and I have used Calibre http://calibre.kovidgoyal.net/ ever since. Its wonderful software in full development with a new release generally ever week.

Have a look at Calibre an open source book management system, which can download chunks of news sites and creates an e-book.It can download the news book automatically. It supports a number of different hardware ebooks. I have a sony prs 505 which is a good piece of hardware.

Meanwhile, I will read whatever is free on my RSS reader that sources over 1000 free sources. I will download them unto my e-paper reader using calibre and you will never see a red cent from me again.

I'm surprised nobody has mentioned Calibre, which was also featured on Lifehacker sometime back.
It is based on PyQT (as well as dateutil, mechanize, lxml, BeautifulSoup) . They even have a CoverFlow like interface which is pretty good. I suppose it is usable on Win, Lin and Mac.
You have to provide a login/password to librarything (or a few other alternatives) and you can then search and tag for the book's metadata and cover images from these sources automagically.
I personally also use them to archive my PDF's that I download from the internet, tag them, specify authors and other metadata (incidentally, most of the papers that people create from latex do not have any metadata).
I see the developers pushing out a release every week, so it is under pretty active development. I dont know if there is a plan to integrate any indexing features in it, but I suppose the developers are open to it.

I have a Sony PRS-505. I use calibre to manage it. No need to deal with any DRM at all. Calibre will format text and RTF files into the LRF format for the reader. You can also use various online converters to convert from PDF to Word and then use Word/Write to convert to RTF or plain text..

calibre

It works with many readers (sony, kindle etc.) and you can schedule downloads of rss feeds, conversion into EPUB format and transfer to your device all automatically. It's cross platform too. It comes with some 'recipes' for many popular websites but you can add your own, allow for secure login etc.

I switched to it from the bundled software of my PRS-505 and never looked back.

I've had the sony ereader for a while now and I found an excellent cross-platform program to manage my books.

Calibre

It has various cool features like conversion of formats and just recently started adding support for the Kindle 2 I think. the best feature, in my opinion, is the rss feed downloader. I've even contributed a 'recipe' for a favourite site to it's repository.

Now when people say "the technology isn't quite there yet" etc. I think twice. I can't imagine buying a newspaper ever again when every day Calibre downloads every news story off the bbc website, various other news sites, hardware sites and I read it very comfortably (bearing in mind the sony ereader is old technology now).

On the PRS-505, there's an excellent open source management tool for the Sony readers called Calibre.

FD. I do work for Sony, but not in Consumer Electronics.

Have you looked at the Sony PRS-505? Both my fiancee and I own one (I bought one for her as a present, and borrowed it so often that I ended up buying my own), and it satisfies most of what you're asking for. It's not technically "open", but there are examples of people modifying it anyway, and it doesn't require any proprietary software to be installed on your PC. You plug it in, and it shows up as a drive, same as a USB key would. Put the books in the right folder and you're done.

It supports quite a few formats natively, and there's a wonderful open-source program named calibre that will convert/format many other things to the best formats for it. Battery life is great, reading 3-4 hours a day it'll easily last over a week without charging. I'd at least give it a look, I don't really have any complaints about mine.

One thing to note is that Sony has put out a new model, the PRS-700, but it's generally considered to be inferior to the 505. They modified the screen to add touch capabilities and a backlight, and it's not nearly as nice to read on.

I got a Sony PRS-505 for Christmas, and it is perfect (IMHO). I use Calibre to manage it, instead of the Sony Software. I charged it when I got it, have used it at least 5 days a week since then, and haven't charged it again yet. Most of my books started out life as .TXT files, before I converted them to .LRF files. It fits in my coat pocket.

The only stickler for you would be the comic book format. It displays images in black/white only, and does not support the comic book format (.CBR/.CBZ) unless you extract them so you get the individual images.

It supports PDF, but I'm not sure how they look as I have never read one on the device.

Hope that helps.

Truth be told, I rather like the situation as it is now: Sony "supports" Windows users while us Linux users have calibre--which allows seamless conversion from many different formats, including Microsoft's .lit and offers library management. Can't say I've regretted buying the Sony Reader. Gotten quite a bit of use from it.

Has anyone used the Sony with this open source program: https://libprs500.kovidgoyal.net/ -- seems like it would make the book management easier.

If you purchase .LIT files, you can strip the DRM using Convert LIT http://www.convertlit.com/, and convert them to Sony's format with libprs500. https://libprs500.kovidgoyal.net/

I'm uncertain of the legality of doing this (for personal use) in the US... see the DMCA exception on the convertlit legal page. Outside the US, check your local laws.

A good source of information is http://www.mobileread.com/.

I have the new Sony reader (PRS 505) and love it. It's sleek, comfortable to hold, easy to read, has excellent battery life, has plenty of storage built in, supports sony and sd flash cards, runs linux, works fine with all OSes I've plugged it into (osx, linux, & windows). You're not limited to DRMed formats either -- out of the box it suports the DRMed and non-DRMed sony format, txt, rtf, and pdf. PDF is a bit annoying with 8.5x11 formatted documents. The BBeB format is probably the "best" in the sense that it makes opening books and font size changes happen quicker than say rtf or txt. Using libprs500 you can convert additional formats to BBeB, most notably html, lit, and (with an additional step) chm. I use mine all the time. In short, it rules and I have no complaints about it whatsoever.

I'm the happy owner of one. After years spent looking at e-books and never finding one whose functionality/price was good enough, i almost found the holy grail. Battery life is brilliant, though something like 10 times less than advertised (i think they advertise 7500 page turns of autonomy, and my experience is that i can read books up to 800 pages on a full charge).

On DRM, the reader's best supported format is the sony one (.lrf files), which provides the best rendering, and which *can* support a DRM layer. It also happens to be a trivial format that also works without embedded restrictions. Therefore, you can download many books from the Gutenberg project in unencumbered lrf format from Manybooks.net. You can also convert many document formats (txt, rtf, html, doc) to unencumbered lrf. PDF support is not good though, as most A4 formatted pdfs will be too small when read in portrait, and will require you to scroll when in landscape. Good enough if you really need to access a pdf from time to time, but there's no way you'll ever read a book that way.

Finally, on accessing the device, mine doesn't work as a usb mass storage device, and i don't know if that's going to happen in the next models (sure hope so, obviously). However, there's a cross-platform open source driver available, which means that since i have the reader, i never had to use the crap software sony provides more than once, just to have a look. Never bothered again, and it doesn't run on my linux box anyway. That driver also comes with a GUI software, and many basic command line tools to access the device (cp, rm, ls etc), and to convert file formats (html2lrf being one of the most useful).

In the end, i really love that 'toy'. The hindrance of not having a backlight on the screen makes it more comfortable on the long run: no more visual fatigue than reading paper. The battery life is good, it is small enough to be carried comfortably (i'm looking at you iLiad), it can read most of the free books out there on the web. The main downside of course, is that you won't get access to the most recent books, as they're only sold with DRM, and usually not in Sony's format. Personally, i wasn't looking for that, so i'm fine, but this *is* a hindrance, and will be until ebook shops change their policies, which could take many years... Ah, and also, it's an ebook reader, nothing else. Well ok, it can display images and play mp3s, but that's really a waste of battery life. It doesn't browse the web, it has no wifi. It's only a book reader. But it's a damn good one.