Goodreader for sure. Sync your documents with Honeysync/Dropbox/whatever within Goodreader. Make annotations, which are a joy to use in Goodreader, provided you have the patience to wait a fraction of a second for menus to pop up (sometimes I do not). Your annotationed copy will be created in your Dropbox folder, or you can annotate directly on the file (the annotations look really good, quite professional). You can flatten then PDFs with annotations if you like and email them to clients or whatever, or make notes just for yourself.
iBooks is a little more slick for reading, but I find that sometimes iBooks brings up blank PDF files for some reason, and you can't sync it to your Sugarsync folder on your desktop/iphone/team members desktop (all at once, collaborative like).
It's hard to overstate how good Goodreader is.