Oh goodness... this is a tough question. Which one of my babies do I love the most? Rip my heart out with the choices!
How about the one I use the most? That would be GoodReader. I love it! But don't take my word for it, read this review too, or this one, or even this one. This little app is one of the best tools for reading, editing, note taking, and modifying PDF's. Even better, you can take a website and make it a PDF from your iPad and then read it where ever as a PDF.
I have used it to carry articles, notes, files, and other documents to the library with me. That way I didn’t have to lug my laptop or files of paper. Everything I needed was one swipe away on my tablet. Then if I needed to make a note I could write or type it directly onto the document and save it. Even highlight the text and draw on the document.
Check it out, for $5 it is well worth it.