I use
Stanza the most, since I hate converting formats, and the Stanza can read virtually all the other formats out there (using the Desktop Stanza to transfer via WiFi).
I have a Kindle, so I use the
Kindle app too (especially since we've figured out how to sync sideloaded mobi books).
BlueFire app for library books, plus all my Sony eBooks (since Sony doesn't have an app yet for the iOS). I hate iBooks and never use it
GoodReader for PDFs (I just use reflow to read on the tiny screen)
and
CHMate for all my .CHM files (works like a dream!)