I've been looking at various note-taking apps for the iPad, and a new one seems way superior in flexibility and in user-friendliness (two things which are not easy to do well at the same time): WhiteNote (App Store link).
Unlike Apple's own braindead "Notes" app, it lets you change font and size, and that's just the beginning. It has search tools, live spell-checking, drawing tools, you can start typing anywhere on a page, etc etc. This is one well-though-out app. I almost never take notes, but this app makes me want to do it.
It's not free, but I think $3 is very reasonable for a good app.