Front to back is more inline with the case's air flow. Bottom to top isn't bad, but the problem is you'll be sucking up air off the GPU if you have one, anyway, which will be much warmer. Without a GPU it shouldn't matter a whole lot.
I actually have all my fans backwards in my 902, so intake is at the rear, my CPU fan blows towards the front, and the 2 front fans are exhaust, plus the side fan is intake and blows right on my two 5850s with Scythe Setsugen heatsinks (very quiet). I also mounted the two front fans in the top 2 slots, so my DVD drive is at the bottom of the case.
Good point on the gpus. I hadn't considered this impact. I'm running gtx 460's in sli. If you think bottom to top would suck too much air from the gpu's, I'll probably install front to back.