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After tying both, I'm using GoodReader mostly. It's interface is unobtrusive, and frankly, less "discoverable" -- you'll want to read the manual. But I much prefer it's reading abilities. With the latest, it can save the highlights etc. back to a pdf even an encrypted one which sealed the deal for me.
I do think iAnnotates controls are easer, but more obtrusive. I prefer it's "select a highlighter" and then "color" over what you what highlighted to GoodReaders "press, hold, move the selection bars, choose highlight". but it comes at the cost of having the tools visible. Well, you can toggle them, of course.
Both are good products and I could be happy with either. Good Reader being $1 and iAnnotate being $10 -- there is just no feature to justify the price difference that I know of.
Lee
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