A few months late to the party, but I've just re-evaluated the cooling on my desktop and having spotted this thread whilst doing a search on the subject I thought I'd add a little to it, so please excuse the bump.
I'm using the best of both worlds, positive AND negative pressure. My system is a bit dated, although the only limitation I'm having is the older slower HDDs, but as a poor student I can't afford better.
I've a 120mm Arctic F12 3 pin on the front and an 80mm F8 3 pin on the lower rear corner on one side. Both are connected to the Motherboard (ASUS P5Q-E) on separate channels, and are set to "Turbo" in Q-fan. They're completely silent, or at least I can't hear any difference whatsoever regardless of what setting I have them on, so I've put them on the highest,
Then I've got an F8 Pro PWM exhaust on the rear which shares the 4 pin PWR header with the CPU cooler (stock Intel which is enough to keep my C2D E4500 cool at 3.0GHz, but there's an Arctic Freezer 7 Pro Rev. 2 in the post so I can put the fsb up to 400 and have a 1:1 dram ratio), and finally the PSU is an OCZ StealthXstream2 600W which exhausts out the rear at the top of the case (no top facing exhaust port in this one).
Because the exhaust fan shares with PWM header, at low load & idle (i.e. when browsing or writing assignments) the flow is reduced and the intake flow is greater than the exhaust flow, so positive pressure. This means most of the time I'm keeping the dust at bay when I don't need the best cooling power my setup can provide. Conversely when I'm doing CAD work (Engineering student) the CPU and exhaust fan speed up together and the exhaust flow is more than the intake, so I get the better cooling effect of negative pressure, only when it's needed.
It's been running like this for a couple of days now and using some thin paper to test it, I've visually seen the difference between negative and positive case pressure. By holding the paper over some of the 'fan-free' vents that air can be drawn from and seeing whether it's attracted to or pushed away from them - there definitely is a switch from negative to positive under load. Just to be safe though I've covered all purposely designed vents on the case with
this stuff (with the exception of the exhausts, naturally) to minimise dust intake. That said even using that stuff there was still some dust ingress using my previous negative-pressure-only setup of a single 12mm exhaust fan + PSU fan and no intake fans, which is what encouraged me to make the switch.