Here's what I'm starting with:
Motherboard = ASUS Sabertooth 990FX
CPU = AMD FX-4100 Zambezi 3.6GHz Quad-Core
CPU Cooler = Corsair H80
GPU = ASUS GTX570 DCII 1280MB
Memory = 16GB G.Skill Sniper (PC3 14900)
PSU = OCZ ModXStream Pro 700W
Harddrive(s) = (1) OCZ Vertex 3 SATA3 120GB, (1) SATA Western Digital Caviar Blue 500GB
Case = Cooler Master HAF 912 Plus
The fans I have to work with:
2 x Cooler Master 200mm
2 x Cooler Master 120mm
2 x Corsair 120mm(with the CPU cooler)
1 x G.Skill fan for memory
I also plan on getting THIS KIT to make it easier to limit the dust in my system. The only other consideration I have is I may end up putting a window on my side panel and aren't too sure if I plan on putting a fan in it or not. I'm curious what others may have to say about keeping a positive pressure environment to keep the dust out as I live in an older building and it is definately a factor.
Honestly the best way to keep dust out of your case is to occasionally open it up and use a compressed-air duster.
There've been long debates about the effectiveness of positive vs negative, but I have yet to see anything conclusive (the general consensus seemed to be try to match input to output as much as possible...)
If you get that kit, you'll probably have to clean those out even more regularly than you'd have to clean out your computer without those...
So I'd keep the two corsairs on the CPU cooler, mount one each of the others as input and output so you'd have a relatively matched system.
I'm not sure about the layout of the case, but generally in through the front/sides, out through the top/back seems to work well...