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I don't really use iBooks so meh. Besides, it's a hassle transferring stuff via cable. I really only do that with my PRS-350 (maybe once every two months so I pretty much transfer as much of my library as the device can hold). The rest of the devices get their stuff via wifi.
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You *can* sync over wifi now with iOS 5. I do it all the time. The trick being you have to be on the same wifi as your computer.
As an alternative for when I'm not home, i also keep my entire calibre library stored in my dropbox folder, so I can download anything sitting in calibre wherever I am. I even pulled my daily news downloads every day by this method when i was overseas. I use ibooks when I do this, but dropbox gives the option of opening in any of the ebook reader programs you've got stored on your ipad.
I think something similar can be done with the whole Calibre 2OPDS thing and Stanza, but I had issues setting that up (most likely due to my own technological knowledge limitations). For me, the dropbox method was simpler.