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?"
Rather than going Microsoft, maybe you should use freemind. I've been using it the last six months on Linux and Windows, and am very pleased with it.
Open source offerings in this area are slim to none, and I've tried everything I can get my hands on. The best I've found is KeyNote, a Windows-only tabbed notebook/hierarchical outliner. I recently converted all my text-file notes over to KeyNote, and found it to be a sweet little package. Highly recommended, although it doesn't really meet any of your other specifications (no hyperlinking, etc., outline-view only).
If you don't mind a web environment, Wikis provide easy editing and hyperlinking, but visualization is not their strong suit. If you like the idea of wikis, but don't want the web, and don't mind paying $12 for closed-source, WikidPad is an excellent, flexible, Windows-only option (and mildly extendable with an embedded Python interpreter). Combines a tree/outline view and Wiki-like syntax & automatic hyperlinking.
If you don't mind closed source, The Literary Machine provides a lot of power in a Windows environment. The basic version was free last I checked, though he's ceased development on it in favor of the Pro version ($20), which is being actively developed and integrates a number of new features (but I haven't tried it yet). It organizes everything based on a non-hierarchical keyword association system, and while it takes some getting used to (and can be downright messy sometimes), it does allow for the discovery of connections between notes that you might not have put together otherwise.
If you don't mind closed source, paying through the nose ($145), and OS X, then there is one app which fits all of your other qualifications: Eastgate's Tinderbox has powerful hyperlinking, programmable agents, RSS and web integration, powerful search, graphical visualization, and plenty more. To tell you the truth, my next computer will probably be a Mac because of this one, though a Windows version is on the horizon (was slated for an early 2004 release, but looks like it's slipped back to Real Soon Now). This has been the sleeper hit of the past couple years--everyone who uses it raves about it, but it's relatively unknown.