I use Calibre2OPDS, which puts a catalog of your Calibre books online for accessibility from the iPad. My Calibre library is also online - both the catalog and my books are in the public folder of Dropbox.
It works well, for me - I can access any book and have it "Open In..." any e-reader app.
The hardest part is the wait to upload all the catalog data info to Dropbox. If you've got a lot of books, it takes a while.
Still, worth it to me. YMMV.
Marilyn
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