To be brutally honest a 486 will likely be more trouble that it's worth. As mentioned you will likely be talking ISA only i.e. will need to track down an ISA gfx card (if not present), NIC etc.
Regarding the hds, even with a BIOS update it wouldn't surprise me to see a fairly paltry limit (137gig max or less I'd imagine). No idea how modern hds would perform on old motherboards either - remember it probably doesn't even have UDMA.
Then there's the hassle of setting up a really old version of windows. To run win2k you need at least a P133 so you'll likely be stuck with Win95b/NT4 (assuming you have a license). Then of course it will be slow as hell with anything less than 32meg RAM at a minimum (not many 486s shipped with that much). So Linux may turn out to be the only option...
My opionion is that it's just simply not worth messing around with anything older than a Pentium2 class system with 64meg RAM. Main thing being with those chipsets you will be getting PCI, AGP, UDMA33, plus of course a system that is capable of running Windows 2000.
A few years back I acquired a decomissioned P133 from work for £1 - seemed like a good deal at the time, slotted in some old EDO simms and a 2.1gig drive I had lying about to beef it up a bit but it was just a waste of time to be honest.