I am currently using ReaddleDocs. It is a multiple format file viewer, while it does not do Epub yet it does PDFs pretty well including one with pictures. It also remembers your spot in all the files you have been viewing so you do not lose your spot when reading. It also has a folder based storage system instead of a flat file system. You can email files both into and out of ReaddleDoc using it browser/email sub app, or save an attachment from Safari to ReaddleDocs.
It currently supports
MSOffice 03 and 07 for Word Excel and Powerpiont
Apple Iworks Pages. Numbers and Keynote
PDF. Htm. HTML. Rtf rtfd
Jpeg jpg png gif tiff
Mp3. Mp4. Mov and a few others
The only down side I have see is no select and copy out of DeaddleDocs and no annotation capability. It is strictly a viewer.
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