- Subversion - With CVS, I wasted a lot of time fretting about file names and directory structures, because it was such a pain having to muck with the repository when I changed my mind. I ended up not being able to prototype nearly as rapidly because I spent time trying to plan the overall structure of my code. Sometimes I'd even give up and go off to work on something else. With Subversion I just blithely give things whatever name and directory structure suits me at the moment and keep working.
- Voo2do - This is the best task-list and project management software I've found online so far. It's got the right features and no more: I can give tasks a name, an associated project, and optionally a priority, a deadline, and notes; then I can create custom views over a particular set of projects. And that's about it. Now I'm keeping all of my to-do lists for everything in one place. Since I've been in grad school, I've found I do a lot of task-switching between my various jobs, so being able to keep all my tasks listed in one place should help me maintain my priorities not just in the context of one job but amongst all of them.
- Procmail - You've just gotta keep separate folders for emails from separate projects.
I'm still on the lookout for good calendar software. Ideally online and compatible with Apple iCal.