The 486 occupies an interesting position in computer history, namely the transition to 32bit bus architectures which were needed to catch up to the capabilities of the post-286/386SX CPUs. The 386 limped along with a 16-bit ISA bus but the 486 had a smorgasbord of 32-bit bus options: VLB, EISA, MCA, and finally PCI.
This is part of the charm, I think, of a 486 build. PCI machines are bloodless; build a Pentium. MCA is right out. EISA is fiddly and relatively rare, so that leaves VLB -- the 32-bit extension bus they stapled onto ISA slots using connectors left over from the MCA bus but flipped around.
So find yourself a nice motherboard with 2 or 3 VLB slots. They are all over eBay. Just about all of them will support a DX2/66. Make sure it has cache. Avoid OEM boards that don't come in their native case.
Memory: 30 or 72 pin SIMMs. Usually one or the other, sometimes both. 30-pin boards should require 4 SIMMs to a bank for 32 bit data width.
CPU: Socket 3 boards are the easiest to work with and probably only have a single socket. Older boards with a separate "math co-processor" socket are just playing games with a 486SX upgrade path -- ignore it.
BIOS: A unicorn board might have a MR-BIOS on it. Otherwise you might not be likely to have LBA support for drives > 528MB. In the world of CF cards, I don't find this a significant issue on a 486.
IO Card: Find a VL SuperIO card that will support up to PIO4. DTC2278s are popular, I think.
Video: FInd a VL VGA card with a respectable chipset like CL542X. Avoid "windows accelerator" cards that ignore DOS performance. Windows will be fine anyway.