[itimpi]

It is easy to get books into iBooks using the Calibre "Connect to iTunes" feature. This is the closest equivalent to the USB connection for a physical Kindle. However is does not work for other eReaders on the iPad. For USB transfer to other apps you need to use iOS file sharing in iTunes.

If you are using the Kindle app you can still get books by emailing them via Amazon.

Another possibility is to pull them on demand into any eReader app using Safari and the Calibre server (or an equivalent such as a calibre2opds catalog).

You can also use a syncing service such a sugarsync and Dropbox, saving the files to a folder managed by the syncing service from Calibre and then on the iPad use the Open In option to transfer the file to the reader app.