Remember that you want to try and put the antenna nearest the center of the vehicle (and highest) as possible. Again, as others have said, this largely depends on the type of vehicle you have and how much permanent modification you want to make on it. I recently redid my antenna system in my car, which included making a permanent mount for my Larsen dualband antenna. This constisted of drilling a hole in the center of the trunk and installing a simple NMO mount. I also re-ran RG8 cable through the car, instead of the more typical RG58. The results? I have noticed a significant performance increase! Stations come in more clear than ever (that's likely due to the much lower line-loss from the RG8 over the RG58). However, transmit is also quite a bit better...
Why the center of the trunk? The metal on the vehicle acts as the ground plane, so if there is a 'balanced' amount of metal on 'each side' of the antenna, then you'll get more omnidirectional performance. This is one of the downfalls from trunk lip-mounting an antenna on the side of the trunk... You'll more get energy directed forward and opposite/across the car (there's more metal in that direction) than rear and on the same side. Thus the benefit of mounting in the middle of the trunk...
In my opinion, the most important factor is putting the antenna as high as possible. For that reason, the middle of the roof is often the best location for an antenna, as it's both the highest spot on the vehicle, and it's as centered as possible. From field reports I've seen, it's signifcantly better to have a mag-mount in the middle of the roof than to have a permanent mount on the trunk. So that means location is more important (in the roof vs. trunk case) than mount type... The best mount option? Permanent mount in the middle of the roof... Then again, remember that when you're in the middle of nowhere, a long rod of metal on highest place on your vehicle also makes it a very good 'lightning attractor'...