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Calibre won't see your Galaxy Nexus because the Galaxy Nexus doesn't appear as a disk drive (i.e. there is no drive letter when you look at the GN in Windows Explorer. The GN uses a newer, more sophisticated communications protocol called Media Transfer Protocol, which according to Microsoft is the best thing since sliced bread but has broken the vast majority of file synchronization products.
There is an immediate solution, and it's a good one that lots of us in the Calibre threads are using. Check out the threads on Calibre Companion. Note that the product is still in it's early stages, but the authors are very active in the threads and have been very responsive to user suggestions and bug reports. It's already a very useful solution.
For a long-term solution, word is that Kovid Goyal is working on adding native MTP support to calibre, but he always has LOTS of stuff on his plate so I wouldn't hold my breath looking for this particular feature in the immediate future. If you can wait a while, you might see what turns up, but otherwise Calibre Companion is $3 well spent.
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