First step: De-dusting. Take off the shielding and blow it clean with some compressed air.
Next: G4FanControl, lower your fan's speed/temperature threshold. It will keep it running nice and cool. (albeit a little louder, but compromises compromises...)
The holes above the hard drive wouldn't do very much, as the HD usually doesn't come above 35C, even during heavy use. If your 250GB drive is a 7200RPM, you should do a test run with high disk activity to see what temperature it averages.
As far as heat-pipes go, the GPU would be a good target. It's the hottest running component in that system. Added to the fact that there's ample space within a 14 incher for some improvement on the cooling.
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