I was listening to This Week In Tech today and I think it was Robert Heron that mentioned a tip he got from Yoshi regarding your computer case. Keep the fan pressure of the intake fans higher than the output fans. By doing this, you don't get dust getting pulled in through every little crack in the case. In the case where your intake fans have a filter, that means you should have virtually no dust in the computer.
Unfortunately, my case, and I suspect most others, have more output fans. I have the power supply plus three others, and only two pulling air in through the filter. That's why I have nasty dust build-up around the floppy and CD drives. I suppose I could get pots to adjust fan speed, but the current setup does expel a whole lot of heat and I'm not sure I want to mess with that.