+1 on Xournal, as that's what I use.

Depends on your style, of course; maemopad+ looked cool to me, but seemed semi-finished feature-wise (lack of editing capabilities) when I tried it almost a year ago. Probably worth a shot now.

Lcuk's got a demo out for his high-performance graphics library, which has an interesting note-jotting mode; I haven't had the chance to try it yet.

I've heard of a guy on campus here who takes a laptop to class, and types all his notes up live in LaTeX; the N800 would do awesomely at that, but it depends on mad TeX skillz, which I haven't...