Idea Management/Navigation Software?
"The system should be hypertext-based, allowing explicit links between nodes, but it would be nice if it could also derive some relations on its own. Having built-in support for referencing web links, printed publications (BibTeX integration?), and arbitrary files would be great. Text-based and perhaps also non-text-based searching capabilities (e.g., graphical visualization of node relationships) would also be very useful.
I've looked at some wiki systems but the choices seem overwhelming, and most of them are geared towards collaborative rather than individual work. Is there some wiki or database system that does what I need, or should I be looking for something in an entirely different paradigm?"
If you're running Windows, it's at least worth checking out. http://www.thebrain.com
I use Memo Plus on the Palm, which is merely a hierarchical notepad.
I have things sorted into a hierarchy that works for me.
But oh, how I would love a cross-platform product that offered deep integration with email, address book, bookmarks, calendar, and random notes, with multiple hierarchical and/or directed graph maps, and good search capabilities. In my fantasy world, it'd run on my PC and on my Kyocera smart phone, and would be compatible with stuff on both ends: Firefox, Thunderbird, the Palm address book, etc. If I didn't have a job, that's what I'd be building right now...
Eloi, Eloi, lema sabachtani?
www.fogbound.net
If you have not seen this program, Check it out. It is a mature product, not open source however http://web.singnet.com.sg/~axon2000/index.htm
Some people think The One True Way is to use outliners. (shrug) It depends on your work style.
... lists a bunch of Windows outliners, along with personal opinion on usage and features.
This really useful page...
http://john.redmood.com/organizers.html
I have been in your exact shoes and have installed Twiki and have the following generalization...
Wiki's aren't as easy to use as they seem. When using a wiki, there's actually a very distinct (but non-obvious) obstacle course between the urge to write and the actual start of writing and it negatively impacts your productivity more than you realize.
... but that's just a generalization from my own experience. I'm still a believer, but not a user.
"Someday, I'll fix it."
Extra comments: Jot + serves me well as a catch-all sort of scratchpad... I'm only an Alt-Tab away from writing, and I also like its indentation model.
The folks behind The Brain are patent fuckwads... they actually patented the idea of using lines to connect thoughts. Avoid them.