What variable in the operating system determines the fans in OS X?

Right now my fans have been spinning for a couple of hours.

However, the cpu usage is low, nothing seems to be running, spotlight is not indexing, all the diagnostics i can think of tell me not much is happening except i have a few connections open.

I know the fans turn on because of heat, and indeed the heat is high on my laptop right now. Yet, I don't see an actual cause for this. What am I missing in my search?

You might want to download Temperature Monitor (free). It will help determine which part of your system is hot (CPU? GPU?), and when things warm up.

I also recommend you investigate your logs using Console (found in your Applications/Utilities folder) to see if there are any unusual errors which seem to correspond with the temperature spikes.

I would shut down, let it cool off, and observe the logs/temperature after restart to see when the fans kick in again.

Good luck.