What the subject says, really. Eclipse and IDEA both have really cool templating features for new classes to set up things like default doc comments and copyright notices and so on. Unfortunately, they set them up on a global basis, not per-project.
This is a Bad Thing, because different projects rarely use exactly the same templates.
Of course, maybe I'm just embarrassed because I was working from home yesterday, and managed to check a bunch of files into CVS with my standard boilerplate "This is my code, why are you even reading it?" license at the top.
For Eclipse I try and have a seperate workspace for each project I'm working on. Then the template prefs stay with each project.
And per-project code formatting! (I think Intelli-J does this, but Eclipse does not).
(The separate workspace idea has some merit).