A Cocoa-powered desktop wiki like VoodooPad, but with revision history for each page, so I can make a diff between revisions (preferably a really cool diff like Xcode has).
An outliner sort of thing where I can drag in a bunch of files as aliases, assign a bunch of metadata tags to them, and then create smart folders of them. I just have way too many uncategorized folders and hierarchical thinking doesn't work for me.
A better todo list application that doesn't lock me into hierarchical thinking. I'm actually working on writing this one. It'll be cool.
Online issue trackers like mantis should have desktop counterparts. I'd like one of those, too.