I've tried both and while iBooks has a prettier display of titles in its bookshelf, in all other ways, Goodreader is better. It's faster, it has better file management abilities, and like others here, I find the cropping feature alone to be a reason to use it. It makes a big difference in my ability to actually be able to read PDFs at full-screen zoom settings.
I also like the fact that I can directly transfer files into GoodReader from my Dropbox or from other sources (even a direct transfer from a PC over wifi). Yes, I can transfer into iBooks via the Dropbox app, but GoodReader's approach is faster.
Personal taste is a wonderful thing, and if anyone prefers iBooks, terrific. I just think that at $0.99 for GoodReader, it's worth at least trying the thing out.
Last edited by dwharrison; 08-13-2010 at 10:45 AM.
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