The longer it runs at a higher speed, the shorter your fan life is. SMCFanControl is not a toy.
I use it on occasion when I have my MBP in my lap and it gets too hot for comfort because it's working on something; I might crank it up to 4000RPM until the temperature goes down, but within an hour I turn it back down.
Note that fan speeds are different across the generations -- my Core Duo's default is 1000 RPM, whereas the Core 2 Duo non-unibodies default is 2000 RPM and won't go any lower than that.