I've seen that sort of thing being done before - the rock project on procooling has 2 fans on the bottom of the case.
The only possible problem is the fans can possibly take up some pci slots. I personally don't like side fans either - I have thought about this before
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2x P3 1100's at 1400, Abit VP6, 2x Corsair 256mb PC150 sticks, 20gb 'cuda ATA-III, 2x 40gb 'cuda ATA-IV in raid 0. 20" Trinitron. No fans
2x 2400+ at 2288mhz (16.0 x 143), Iwill MPX2, 2x Kingmax PC-3200 256mb sticks, 4x 20gb 60gxp in Raid 5 on a Promise SX6000. Asus Ti4200 320/630. Cooled by Water
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