Do you want to handwrite your notes (with a stylus)? Or type them?
Of the apps I used, I liked iAnnotate for handwriting + stylus.
I also liked Polaris office. It was one of the few that I found was able to display/edit both the speaker notes and the powerpoint sections on the same page. I have speakers who put extra information in their speaker notes section and I also like to type up my notes in that section so having easy access to both as a big plus for me. It was pretty much the only app that had this feature for me (at least when I was looking).