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I have tried a lot of the free PDF readers out there and finally settled on Apabi Reader. It is free, fast, and renders the PDFs nicely.
 
GoodReader is a great app to have to manipulate PDFs and other files (zip, wmv, others).

That all said, I still like iBooks. It seems to render faster, and I prefer horizontal page turning. It also does TOC better, IMO. You can use GoodReader to move PDFs to iBooks.

In any event, iBooks is free, so it's well worth checking out for PDF use. I would also strongly recommend buying GoodReader - it's a great tool to have and integrates well with Safari and Mail.
 
Really depends on your use. If all you want to do is read PDFs, Ibooks is very good, better than goodreader in some important respects. But Goodreader has really come along way over the year and now includes many features such as a very complete set of annotation tools, file sync properties, conversion of docs to pdf, opening zip drives. So for the causal reader, Ibooks if great but if you really need to work with pdfs, cough up the $5 and skip Starbucks for a day.
 
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