Been trying various note taking apps ever since I purchased the iPad. I think I have about 10 on my iPad at the moment. A few points.
() Keep your priorities straight. Do you want to take handwritten notes? If so, is that your primary or secondary priority? i.e. Are you going to type for the most part and just want the ability to add a quick annotation or a diagram or do you expect to write by hand/draw and just want to add a readable typed few lines to your drawing/handwriting? If you need to capture diagrams and drawings, look for an app that can turn a squiggly scrawled box into something cleaner. If you're taking notes on Shakespeare, that may not be very important.
() Is organization of your notes in categories and folders important to you? Some apps support that approach; others are "flat" in their organization.
() Do you want to take notes in sync with audio? If you're recording a lecture that may be important. If you're keeping notes in a meeting, it may be worthless.
() What do you want to do with the notes when you're done? Be sure the app you choose can export the notes in an appropriate format to a destination you can use.
() Do you want/need handwriting recognition? If you are as bad at writing on the screen as I am (even with a good stylus) it may be important to have an app that can transform your scrawl into something others (and even you) can read when you're done. Some recent apps provide excellent handwriting recognition but lack other crucial features. I've been using 7Notes HD Premium lately and find it to be extremely good at capturing and recognizing my handwriting and transforming it into readable text. That functionality combined with its predictive word recognition makes it almost as fast as typing, but it takes awhile to become proficient. (See note below about PRACTICING!)
() If you're typing notes you may want more capable word processing features that enable you to "clean up" notes into a more formal output. If so, consider getting a full scale word processing app and use it for notes. In fact, if you're a good typist you may not find ANY note taking app is as useful as a good word processing app.
() Whatever app you choose, PRACTICE! The most comprehensive and capable note taking apps (e.g. Notes Plus and Note Taker HD) call for lots of practice to use effectively. An app that seems simple to use in the first half hour may fail in terms of other features. Conversely, it may be difficult to use an app when you begin but after awhile it becomes more intuitive. Think how long it took you to learn to write. You weren't adept at it in a few hours. Whatever you do, DO NOT take a new app to an important meeting or a class and expect to be able to use it effectively. The stress of trying to keep up with what's going on and learning to use an app at the same time will only lead to frustration.
() Finally, be prepared to invest a few bucks in your search for the app that works for you. The best apps are truly remarkable pieces of software and developers deserve to be compensated for their efforts. And don't expect others with different priorities and different abilities/backgrounds to advise you about the "best" note taking app.