Have there been case studies of how anonymous bitcoins are? The blockchain has a lot of information about all bitcoin transactions.

I've heard a lot of conjecture about how anonymous bitcoins transactions are, but I haven't seen a scientific study.

Are there any case studies that show how to track a bitcoin transaction to an individual person? I see IP addresses on blockchain.info so that information could be subpoenaed; on the other hand, you could use Tor which also has its documented weaknesses.
Yes, the most notable one being this one. It illustrates that it is possible to associate transactions and addresses with forum users' identities, as well as connecting them to some organizations (including WikiLeaks, MyBitcoin, Slush's Pool etc).

Tracking users by their IP is a bit harder, although during the work on my master thesis I was able to find an IP address associated with a Bitcoin Address and trace it correctly to the Bitcoin Faucet.