I've had this problem a lot as well (reboots from 3 to 15 min playing time). Most symptoms during crash or reboot seemed to suggest dodgy graphics card. After investing in slightly newer card, I noticed my graphics were smoother but I still had the problem. I didn't bother playing with drivers or trying to run barebone.
I won't go into details about how (as I'm sure everybody knows how time consuming that can be), but it turns out in the end that my problem was my CPU.
Civ4 tends to overheat my processor something fierce

Not having the time (or inclination) to search for a new cooling solution, I opened the case and turned a good old fashioned fan on to it.
Civ4 has now only rebooted once in the last 15 hours or so of playing time (on a large map)
-Oci