I switched over to taking all of my notes at scientific meetings on my iPad a year or so ago. In my office I actually use a Livescribe pen, and always have one of those and a small notepad around but the small notepad isnt great for taking a lot of notes at a meeting, more for jots to myself about stuff.

The apps I use are NoteTaker HD and recently I have been testing Notability. I have tried many others, and Notability is the only one that comes close to NoteTaker HD in my opinion. The nice additions to Notability are that it does record sound as well.

With both apps, I use a Boxwave stylus to hand write my notes. I can then mail them to myself as PDFs when I get back to my office. I like the smooth rubber tip on the Boxwave stylus more than the foam type tips a lot of other styli for the iPad have. The great thing about both of these apps is that they have a window to write in, fairly large window in fact, and when you write in it the text is put in a second window on the page, and shrunk down. The net is that you can write fairly large, important in my experience with a stylus, and it is then stored compactly on the page.