It might be the RAM, like Barney says, I remember reading about dozens of cases that boiled down to RAM and other hardware problems. I once had a PowerTower Pro that complete froze (again and again) because of a ISDN router that had a bad firmware update.
About my Mac Pro kernel panics: It was about 5 years ago and exactly because I tend to forget the specific details, I sometimes write an article about it: http://beeldbuijs.nl/how-to/mac-pro-problems-solved-by-lion/
I had all kinds of weird problems, from the keyboard that would sometimes stop reacting to kernel panics to the Mac Pro waking up by itself in the middle of the night. However, those things usually happend only once in a few days, making it impossible to tackle. At one point I thought it was de RAM, at another the keyboard, but replacing them didn't solve it.
Finally, I did a clean install and didn't use migration assistent out of fear of restoring the bug as well.
I used a fresh installation of 10.7 Lion on a FireWire external hard drive, so I could try it out without messing up my daily system, that was still 10.6 / Snow Leopard. That fixed it, so I then installed Lion on my internal HD. I have only experienced this type of problem once since working with Macs since 1995.