MySQL has so much cache by default I don't see much of a difference on EQEMU between 5400rpm and 7200rpm. Even stripping down MySQL to only cache InnoDB and MyISAM there is still more than enough software cache to deal with the persistent reads/writes.
Based on my own testing (on a P4 2.4C@3.0GHz originally, to try to mimmic PEQ) RAID0/1 on the ICH4 controller isn't so hot either. Semi-modern RAID5 seems ideal (on a Dell PERC5 or Areca controller anyway, your mileage may vary) regardless of spindle speed, and it provides the user a little bit of breathing room (OH NOS THE HARD DRIVE DIED! I LOST IT ALL!) but does not replace good backup methodology, which is important with this kind of server!
Please keep in mind that some onboard video solutions (VIA Unichrome comes to mind) eats more amps/watts than an el cheapo PCI ATI Radeon 9200. And most BIOS solutions force you to use at least x megabytes of memory even with the damn thing [onboard video] disabled. Old Matrox Millenium cards have always been my favorite, they're low wattage, small form factor, will run without a heat sink fan and they have a great RAMDAC for 2D imaging, not very much of a filter on the colors so everything is really bright, their output is 1.1v standard and they're usually about 16 megs VRAM. Also, if you're working in a 32-bit environment (P3/P4 architecture as stated) the video memory (including onboard reserved) tends to chip away at the user usable RAM once you near 4 gigabytes even in the most advanced PAE model. 3 GB RAM + 512 meg video card == losing some addressable regions in the OS for anything but kernel and driver functionality.
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