Firstly, do a search, there are lots of threads on this subject, and many of them have helpful pictures illustrating their installations.
That said, this has been an issue for me as well. For now I am using an el-cheapo mag mount that lives in the garage unless I'm wheeling, but I plan to install a 2 meter ham radio in my rig and I will want a more permanent installation.
Many have mounted their antennas on the rear quarter panel. I've also seen some mounted right above one of the taillights. This is okay for keeping the antenna out of the way, but not the best for signal propagation.
The center of the roof is the very best place to mount an antenna from a radio wave perspective. The sheetmetal roof provides a good groundplane and keeps the RF energy out of the cab for the most part. The problem with this installation is breaking your antenna on tree limbs or overhangs.
I have thought about mounting my antenna to the front bumper. It seems like this would put it out of the way, I would be able to see it so I would know if it was going to hit something, and it seems like it would work reasonably well, other than putting ~50W PEP into the cab.