Can a Bitcoin server have a .onion ToR address? Is it possible for a Bitcoin server to have a .onion ToR address?  

If so, are there any in existence today?

(Note: this is an alternative to hiding addresses via the Azure Service Bus)
Yes, since version 0.7 this is possible with the reference client.

See the documentation about tor: https://github.com/bitcoin/bitcoin/blob/master/doc/tor.md

EDIT: also see https://en.bitcoin.it/wiki/Fallback_Nodes#Tor_nodes for a list of published onion nodes. The explanation on that site should be updated to reflected the built-in support for onion addresses since 0.7.0, though.