The Kindle app is probably my most used for MOBI files. I keep my Kindle in my car and my books are always in sync on the right page on my iPad or my physical Kindle, so on the go I've always got my books even if I don't have my iPad.
Comic Zeal is great for comics and PDFs. It's got decent hierarchical folders.
iBooks is good for PDFs and EPUBs, but since it syncs, I tend to not use it as much for documents I don't need synced.
I keep PDFs of all my product manuals on my iPad, very handy, especially when traveling. But there is just so much clutter of manuals, newspapers and other types of PDFs, I'm tempted to start using different readers for different documents. Manuals in one, magazines in another, reference (dictionaries, fact books) in another.
The Adobe reader seems a little slow for PDFs with images. Page turning drags for the few things I've tried.
Anyone know of an eReader that will open DropBox or Box.net cloud storage?
Gary