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I have to say, iAnnotate edges out Goodreader as my favorite.
It loads PDF's faster, offers smooth vertical scrolling, and has more intuitive, expansive annotation tools. It also syncs with Dropbox and other cloud services in an easy fashion.
Goodreader can't even display continuous flow across pages when vertical scrolling! And iAnnotate is "best in class" in terms of loading PDF's FAST.
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