I don't know what the onboard chip is. The separate PCI Adaptec is undoubtably top-of-the-line ... but the onboard chip may be an Adaptec also (though maybe a slightly older one.) No idea. It works with Linux, that's all I care about. My personal webserver has an Adaptec SCSI interface but then again I got the dual, non-SCSI board for pennies (thanks to Mike Sisk of Furfly.) If that hadn't been true, I would've bought the motherboard with on-board SCSI for an extra (at the time) $200.
I haven't investigated modern SCSI (my server's board is UWII, we've passed U160 and are at U320 or whatever) so the separate board may offer two channels or other high-end features you might need if you plan to add a half dozen 36 GB drives :) Onboard SCSI usually offers one highspeed bus capable of handling 8 devices (but again I haven't checked in a long, lnog time) but in this case the tiny tower case rules against putting that much stuff in anyway.
Onboard SCSI has been the choice for rackmounts for years now along with onboard NIC. The only thing missing is the external plug for adding external drives, but if you're looking for that much storage, you probably want a more robust server anyway (this one has four internal bays for drives, though using two is probably best for cooling purposes)
