I use
Comic Zeal for comics (its great, specially if you get your comics from "alternate" sources

).
For straight PDF reading, I use
GoodReader (and it excels as a TXT reader as well - great for Gamefaqs!). If I need to heavily annotate the PDF (as is the case with scientific papers and textbooks),
iAnnotate PDF is the most robust solution I was able to find.
But you can't go wrong with GoodReader. Its a must-have app.