There's a useless fan filter inside the power supply which is worth removing. I say useless, because it's on the wrong side of the airflow to stop dust getting into the 6100. All it can really do is collect dust, clog up, and stop the 6100 from cooling itself. If you were really keen you could replace it with a filter at the air intake under the hard drive.
You'll need to dismantle the power supply to get to it. Be careful. If you don't want to do that, at least pull the PS out and vacuum the dust out of the filter.
One other mod I've done was a strip of foam across the underside of the case, to separate the air intake at the front from the hot air outlet at the back. That seemed to help. Having them both blow into the same cavity always seemed a little dumb. If you turn the case over you'll see what I mean. Try it with a rolled up cloth first. I used self-adhesive draft stopper foam, diagonally from the front floppy-side case foot to the rear Nubus-side foot.
It would also be worthwhile re-doing the thermal paste between the CPU and heatsink. No doubt this has dried out by now. The heatsink clips are accessible from under the motherboard.
If all of the above fails, try to find a small, quiet fan to sit in the top of the heatsink. The ones that come with the Output Enablers overclocking kits wedge in there pretty firmly, and I think they're from 486s or something.