Calibre is the leading ebook and ereader management tool. It supports conversion from and to a wide variety of eBook formats. It will also assist you in organizing your ebook library and transferring them to your ebook reader (almost all are supported).
Much to my surprise, earlier versions of calibre didn't support the TouchPad. considering that calibre usually supports even obscure devices right after they're released, the fact that the TouchPad wasn't supported until after it died should tell you a thing or two about its lack of success.
The new support only extends to the Kindle app; the other 2 reading apps that you can currently use on the TouchPad, Adobe reader(PDF) and pReader (Epub), aren't supported yet.