Now that GoodReader is updated, would anyone be able to chime in on how it compares to iAnnotate? Narrowed it down to those two!
iAnnotate generally has a larger feature set. The question then is whether you really need those features or not. GoodReader does all the basic things you can expect from a pdf annotation tool, and does them well.
Another difference is that iAnnotate has continuous vertical scrolling, while GoodReader scrolls page by page. I prefer the former for large documents, especially when I work on research articles where I often go back and forth between the main text and the reference list. Again, that's a quite specific use pattern that you might not need.
Another difference is that GoodReader offers a better hand writing experience, because it has a zoom box. For some reason, iAnnotate doesn't seem to want to add this feature to an otherwise rich set of tools. I find it extremely useful for making up pdfs.
There may be differences in how they sync (one sync versus two way sync, selective sync, etc). I don't know if they are different and if so, what the differences are, but that's something to consider.
Finally, as I wrote in the post I linked to above, a key difference for me has been extraction of annotations. That's the main reason why I now use GoodReader rather than iAnnotate, because iAnnotate jumbles the text, while GoodReader doesn't.