handwriting apps: I'm a fast typer (60-70wpm), but I find I can still input data faster and retain the knowledge in my memory better if I actually write it down old school style. So, this was the first type of app I looked for when I got my iPad. I've tried almost every one in the app store and here is a quick review of the ones I didn't delete immediately for being awful...btw, I use a pogo sketch and after getting used to the different feel from a pencil, I think it works great, although I would prefer it to be a little longer, fatter and heftier (like an actual pen); the fat tip doesn't present any problems because the software translates pretty well to a fine tip.
All of these can organize by file name (class name) and have multiple pages per file. All can share in some fashion. And, except Penultimate, all can combine text, handwriting and drawings together.
1. Notes Plus: My favorite, I like the zoom function that allows you to write with finger or stylus and it reduces the size to the writing surface; the zoom box auto advances on the line and to the next line. With this zoom box, I can put the same amount of data on one page as I can on a standard paper notebook page. Accepts keyboard inputs and exports to email or pdf. What I don't like: the erase function, it erases by event, not like a normal eraser, so you will erase an entire word when you only want to erase the "s" at the end. No audio record, no bookmarks.
2. Noterize: not bad, I like the quick change options for pen, highlighter and eraser, also does keyboard input and audio recording. But, it doesn't reduce the size of your text like Notes Plus and I can't get as much data on a single page. It has a share function with dropbox, google, email and PDF support.
2. Note Taker HD: (yep, tied with Noterize IMHO) A lot of the same zoom functionality as Notes Plus, but too many confusing controls on the screen. I prefer a simple UI.
3. smartNote: not bad, but zoom function is only useful for adding details to drawings, not for writing notes in class. Too many useless graphics (notebook cover, wallpaper, etc.). Does have a lot better interfaces for sharing, widgets for adding things like a cartesian plane, etc...This would be my favorite if it had the zoom function for getting more on a single page.
4. Penultimate: the page size is too small for the pen size...you just can't get as much data on one page as I would like. No audio, no keyboard input. A lot of hype, but ultimately bottom of the barrel for taking notes in class.
If you like handwriting recognition, WritePad works great. It either translates your handwriting to text or accepts keyboard inputs
Ultimately, I use a combination of Notes Plus and WritePad (French). I've deleted the rest from my iPad.