wildbill:
Could it be someone who has (or had) access to the keys just messing with you as a prank? Does the varied state you find your car in rule out John's suggestion or confirm it?Could it be that a bunch of teenagers want some place comfortable to sit & smoke and captured the signal from your remote? I'd expect them to leave some kind of evidence though and it seems odd that nothing has been stolen.
So, webcam is probably the best bet to find out which it is, and better to call the police than go out & engage an unknown number of miscreants (or your ex).
Some webcams come with motion tracking software so they only record when they detect motion. I don't know if the webcam manufacturers care about adding that to a package anymore. Anyway, buy a cam that can record under low light condition and prop it up against your window and your computer should have enough hard drive to record night after night.
One other thing you can do is to get a pair of car horns that sparkfun.com just started to sell and mock up their project. Any movement ever so slightly will set off the horns and scares the persons away.
To make the alarm box noticeable, add a couple of flashing LEDs on the box.