i've wondered about these things, don't they cause your MBP to overheat a bit? What about scratches?
It probably inhibits the aluminum case of the system to dissipate heat somewhat, but I can't see it causing systems to overheat as a result. Fans will run at higher RPM's, on average most likely, causing fan replacements to happen sooner.
I had one on my early-2008 MBP, and when the battery finally gave out on it 2 years 11 months into AppleCare (in retrospect, I had it plugged in more than I should have,) I took the shell off to bring it in to get the battery replaced, and they (Apple Geniuses) were impressed about how the system looked like it was still brand new. So, do they cause scratches? No.
So, possible decreased fan life in exchange for scratch resistance to the system's chassis. It's up to the individual owners to decide if it's a tradeoff worth living with.
To the OP: I'd get the clear. I don't like how the dark one blurs the Apple logo.