I take notes during rotations on my T3 (instead of index cards or whatever). I do most of them in Word To Go, which gets converted to regular Word files on HotSync. You can do color, different fonts, and perhaps most useful, you can put bookmarks in the document. The way I have it set up right now is separate documents for different subject areas/specialties, then bookmarked sections within each for more specific categories. I've also used MemoLeaf, which is sort of like enhanced Memo Pad, mostly improved sorting/filing stuff.
What I'm still looking for is a program that will let me draw next to the typed notes.