I have it set up this way:
Top 1 - Out
Top 2 - Out
Rear - Out
Front - In
Side 1 - Filter, No Fan (my CPU heatsink is too big for me to use a fan here)
Side 2 - Filter, No Fan (that side panel has a tendency to amplify vibration, which is why I don't use a fan here)
CPU Fan - Up, towards Top 1 and Top 2. I've also tried it the other way pointed at Rear. There's not a whole lot of difference. I only have it this way so that the hot air on the back of my video card is pulled out of the case.
* The reasoning behind that configuration is that cool air is drawn in from the lower front and exhausted out through the top and top-rear. Hot air has a tendency to rise, so if you're using the top two fans for intake, that's counterproductive.
* I have a relatively light system. If you're using a quad and a decent number of hard drives, then you might want to add more intake fans. Either jury rig a second one onto the front (or buy another 4-in-3 module). Or use the side intakes.
* Seems lopsided at first glance, but many older systems and cases had no dedicated intake fans at all and got by just fine. As long as the side panel is on, the negative pressure generated by all the exhaust fans is going to help pull in air from the front anyway.
But a caveat - a case with negative pressure helps to prevent heat from building up inside the case, but as Zepper alluded to, it also has a tendency to attract a fair amount of dust. So it's something to keep in mind.