I'll 2nd (or 3rd) the vote for an NMO mount in the roof. I put one in my RAV4 and it currently has a 12" dual-band antenna on it. Not the most efficient, I suppose, but it works OK with the local repeaters and on simplex. Most important to me, however, is that it has never hit a garage ceiling. If I know that I won't be near a parking garage for a while, I have a much longer antenna in the trunk that I can swap out in 2 minutes.
When considering mounting locations, consider how you'll run the cable. with a roof-mounted NMO, the cable is in the car and it's just a matter of running it down a roof pillar (minding any airbags that might be in the way). If you run a luggage rack-mounted antenna (I have one of those, too), you have to find a way to get the cable into the car. That's harder to hide and you have to watch out for water leaking in with the cable.
I know everyone says that a glass-mounted antenna isn't the best (and they're right), but they work (at least mine have). My RAV4 has one of those, too. They are definitely a compromise, but then so is a 12" dual-band antenna (even a roof-mounted one). So, while a compromise, they might still be an option. I would point out that when I mounted mine on the windshield, I had to cut it down a couple of inches because the thicker glass de-tuned it a bit. YMMV, of course.
However, after installing all these different mounts on my car, if I had it to do all over again, I'd just punch a hole in the roof and be done with it (in 30 minutes or less). It's not as traumatic (after the fact) as it sounds (before the fact)
. As WLF said, the impact on resale value is mostly imaginary.