Not directly related to programming, but for documentation reasons I like the free version of XMind (Mindmapping tool) and TeXlipse (LaTeX environment, on Sourceforge, sorry, but could not post a second hyperlink) a lot.
I like some of the previously mentioned ones e.g. Findbugs.
And I second Jay R. that I'd rather use Subversive to Subclipse although Subclipse is easier to install (on the Mac at least).
