GoodReader & Daedalus
I recommend GoodReader for documents. It seems to handle a larger variety of documents and can even tackle the big PDFs (say 500+ pages in full color). It also can read annotations and allow you to make your own and still dump it back out to somewhere else. Phenomenal PDF reader.
Daedalus Touch for text input, manipulation and export. Instead of books, you have stacks of sheets that can be moved around and manipulated (even from one stack to another). It is more of a minimalist approach, but with a lot of functionality. Export is available to txt, pdf, epub and email (print as well). Currently it syncs with MobileMe and Dropbox. I'm sure it's just a matter of time until it syncs with iCloud.
