I'd suggest go with ATX and go from there. The GA-5AX is a good starting point!
When you build a retro rig using the ATX format, you're probably more in known territory 😉
When it comes to what parts to use, theres a LOT of info available. Many good parts can be had for very cheap at this time (I specifically didn't mention "these days", prices and availability is a virulent thing).
Just use any old harddrive you can find cheaply. If you can't find one of the 1337 graphics cards (Voodoo comes to mind) then any old GeForce2MX will do just fine as a start (though I'm not so sure about it's compatibility with DOS). Try to get your hands on an S3 Virge (mostly PCI, 2MB or 4MB and used to be VERY common! And turns out to be of great value for retro rigs actually).
For the case, just use any old ATX case that you can mount a full sized motherboard in.
For PSU's (VERY important for stability, even for such old rigs) I'd recommend to get an old 300W FSP unit (but 250W will do perfectly fine also). Try to avoid the El Cheapo brands if you can. It's not critical, but worth it if you don't like silly little troubles stacking up as time goes by.
Brand new PSU's are not so good for ATX boards with filled ISA slots, it has to do with some of the power rails missing.
For a processor, at first I'd suggest to get any Pentium MMX. They are cheap, available and work on every Socket 7 board.
If you want more, then I'd suggest to get a cheap K6-2/-anyspeed- and if you want MAX, then I'd suggest you get one of these:
http://cgi.ebay.nl/SOKET-7-BOARD-OVERCLOCKING … 0-/140433982225
You'll probably need to flash the BIOS though to support it, but no hurting in trying.
One more thing about retro computing.
These come with JUMPERS to set VOLTAGE, FREQUENCY etc.
You can't just plug in a CPU and expect it to work, so reading the manual IN ADVANCE is critical if you want success.