Best PDF markup: GoodReader
GoodReader didn't start as a PDF annotation tool, but it's evolved into a darned good one. You get the key markup and editing tools you expect from Acrobat Professional. The app is good at using touch gestures for highlighting portions of your PDF for markup.
Our only quibbles are getting the markup menu back can be tricky and you can't rotate individual pages, so sometimes you're marking up a page rotated 90 degrees from the orientation of the sticky note's text you're adding.