I've actually build up 2 high end 486 machines and, believe or not, am still tweaking it (memory, sound card, graphics card and CPU) to find the optimal solution.
However, to due to the lesser availibility of some "brand names", it did take me some time to find those components.
There are quite a number of good brand names out there but, most of the motherboards I have are ASUS and Gigabyte.
You will also have to decide whether you want to go with Vesa Local Bus or PCI.
Some later 486 motherboards had both PCI slots & a Vesa Local Bus slot (with your standard ISA slots as well) but, in this case the Vesa Local Bus slot could sometimes only be used with a graphics card.
A nice feature on some later 486 motherboards was that some of them also came with a PS/2 connector, which then enables you to connect a PS/2 mouse to it (useful in my case as I'm using a KVM switch)
I've read some good reviews about the Biostar MB-8433UUD and, to a lesser extent, the PC Chips M919 (there are quite a number of topics on these different boards).
I have the Lucky Star LS-486E (PCI based) rev D, an Asus VL/I-486SV2GX4 (VLB based) and an ASUS PVI-486SP3 (VLB & PCI based) motherboard.
I've read some posts (just can't track it down now) about "combo" VLB/PCI boards and that, depending on the configuration, PCI performance can suffer (be throttled) due to the Vesal Local Bus.
Based on some benchmarks I've performed, my Vesa Local Bus graphics performance has always been faster than on an equivalent PCI based system.
Most Vesa Local Bus motherboards don't have onboard controllers (Hard drive, Floppy, communication ports, etc.) whereas practically all PCI motherboards do have onboard controllers.
Based on some other posts, most people seem to value the Tseng Labs ET4000 W32/p as a very good Vesa Local bus graphics card but, for PCI cards you have quite an array of cards to choose from (S3 Trio 64 or Virge cards, ATI Rage II, etc.). However, I've had problems getting some of my later PCI based graphics cards to work properly on my 486 PCI motherboards.