Hi. I've tried many of them, and my favorite at the moment (for many reasons) is Note Taker HD. Whatever you do, I'd recommend getting an app with a zoom feature in order to deal with the iPad screen, which really isn't made to handle a stylus. Penultimate is an app I would stay away from, even though many people seem to like it.
As for a stylus, just about anything will probably do, but I've been pleased with my Targus.