Almost all the word processing apps (Pages, QuickOffice, Office HD, Documents to Go) have a PDF export option; if you are taking about creating a PDF. Note, I'm only 100% sure about Pages, since I don't' use the others.
PDF Expert offers the most options to edit PDF files after the fact. It is more limited than a full PDF creation/editing app, but probably the best you'll find on the iPad. It's a solid app with a clean UI, but will take a bit of digging to find all the features.
PDFPen is an up and coming app that is likely to give PDF Expert some serious completion. Last review I read said that it was slightly buggy and was not quite as feature heavy, but more enjoyable to use.
There are at least a couple of good apps to convert other files to PDF, but since I don't use them I don't have any of the app names handy.