Ah, you are talking about PDF books, not ePub. You are right, the links and text selection won't work.
I don't have any PDF files with links, so I can't test; but GoodReader allows you to select text and do a Google search with it, much like I described for iBooks. PDF Expert will also let you select text, but you have to copy it and paste it into the search bar.
Those are the only other PDF apps I have besides iBooks.