iAnnotate is my app of choice for annotating pdf's.
I used Notes Plus for a while for free-form notes, but I'm leaning toward eNote Taker now. The dev is active on this forum and receptive to ideas for updates.
Have you figured out how to remove the iAnnotate footer at the bottom of the doc?
Kinda annoying,
I figured it out.. By default after emailing a marked up doc there's a footer that says 'created by iAnnotate' or something like that.What footer?
I owned a lot of apps for note taking (yes, I am that guy) and I've found that currently the best that give you both features is uPad. Note Taker Plus provides the same functionality but I don't like the UI.
As other, I love Notes Plus and their coming update (end of July) will support PDF annotation. If you can't wait, I recommend uPad.