I have had weird fan issues on my late 2006 MBP C2D for the past 2 years. Not debilitating, but annoying. They'd spin up to 6000 RPM for no reason and stay there for 5+ minutes, it happened all the time. Almost always when I tried to watch any Flash video. The fan control software didn't seem to help.
I suggest you try resetting the SMC, which controls all kinds of low-level stuff, like your battery and your fans.
http://support.apple.com/kb/HT3964 -- I did this but it didn't help my situation, certainly worth a try though.
I finally took my Mac to the Apple Store, they tested it, and found a bad SMC chip. They gave me a logic board replacement (and a few other things, like an I/O board replacement, what the hell is that??). Nice bonus since I have only 1 month left on my AppleCare.
If you have continued problems, let Apple look at it.