Background: I showed Lockitron to my dad a while back, and he wanted it for his car. ie unlock/lock from his phone, or even by just walking up, like keyless-go on the mercs.
I did a bit of googleling, and it seemed like it should be pretty simple. Connect a dongle to the diagnostic port (inc CAN bus wires), and then fire the correct CAN messages down. On most modern cars you can pretty much control anything, from the locks, cruise control, windows, seats, radio, lights, wipers etc. The problem is the CAN message format isn't documented anywhere, and it varies from car to car. You would have to sniff bus, with lots of trial & error.
If there was a high level API, ie openDriverSideWindow(), I could image the community creating a whole host of automation possibilities. ie Open windows when the temp is above 30C, or turn radio down when I'm close to home.