I've been using iBooks to read
.epubs that I've downloaded from the Internet, and made many annotations in them.
How can I export the annotations to another Mac, or share them all at once?
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I think there are two options.
This app is still not yet released http://www.compendiumsapp.com/
The other technique involves an app called Digested. I took the hint from here http://computers.tutsplus.com/tutorials/beyond-highlighting-how-to-get-the-most-from-your-annotations--cms-20013 and should work for your other Macs.
...sync your iBooks with your iOS device, and use the Digested app to copy the annotations back to your Mac. It's a roundabout way, but it does work.