It really depends on if you want to type your notes, or scribble them with your fingers or a stylus.
If you’re a scribbler, like I am, you’ll want to go with Noteshelf. It has the design metaphor closest to real note taking, while offering some advanced features borrowed from my second-place scribbler, Note Taker HD. The only real downside with Noteshelf is that it does not automatically sync with Dropbox, though it can export there.
I use a Targus stylus for my scribbling.
Typers will want to go with Notesy. It solves the Dropbox problem by syncing automatically all the time. Dr. Drang’s review of the iPhone version is the one to read for more info on that, and it definitely applies to the iPad version as well. Dropbox will take care of versioning your files as well.
I’d really like to try “Circus Ponies NoteBook” but the price of $29.99 is prohibitively expensive.