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.