I would advice a socket 7 motherboard with an Intel 430TX chipset. It supports USB and SD-RAM (up to 256mb, but only allocates up to 64mb). It's one of the fastest chipsets out there and the USB works really well with more modern drivers (like the USB2.0 package for Win98 SE).

My own board is a Biostar MB 8500 TTD and I'm pretty happy with it. It's currently got a AT PSU hooked up to it but it also supports ATX (I would need to solder on a connector for it). When looking at board from this era, the USB wasn't so universal as it is today. Biostar for instance, used a different pinout for it's USB header, so I had to modify a standard usb cable to use it.

That could be a very, very long list...

How about narrowing it down a bit:
- EDO or SDRAM?
- how much RAM do you need (<=64MB or >64MB?)
- uniprocessor or SMP?
- how many PCI/ISA slots are you looking for?
- PCB colour preferences?
- size/layout constraints?
- do you want to be able to overclock FSB?

Generally, if you want <64MB RAM, i430TX is the best bet - and gives the most ATX options.
If you want >64MB and/or SMP, i430HX is the only Intel chipset option (er, except the ancient, glacial i430NX), with a fair few ATX board.

Edit:
Btw, i430TX shares memory controller with i440EX, so even though it officially only can do 256MB, it can unofficially manage 512MB (with 16x 128Mb chip DIMMs). However it still can't cache anything over 64MB, which is a minor irritation with WinNT/2k/XP or Linux, but a big issue with DOS or Win9x (as they load memory top-down). For 512MB cached, i430HX with a second TagRAM is the only Intel chipset option.

A few people have mentioned 430TX chipset as a good choice... one interesting board with that chipset is the Intel AN430TX. That's an ATX board, and notably includes Yamaha OPL3-SA3 onboard audio (WSS & SB Pro compatible, use UNISOUND for DOS) and OPL4 (YMF704) wavetable midi accessible via MPU-401 interface. 4 PCI slots / 3 ISA slots (1 shared). I've thrown a Pentium MMX 233 and 64MB of SDRAM in mine, and use it with Windows 98SE and 2K.

There's a version of the board with onboard video (ATI Rage II+) which is probably best avoided if you want to use your own graphics card, since it only has 3 PCI slots.

Thanks guys, I highly doubt I will ever need more than 1 CPU and 64 MB of RAM on this machine. SDRAM support would be nice since I have a large number of PC100/PC133 sticks laying around. So I guess i430TX it is.