I always recommend VLB for anyone who wants a good 486 system. Aside from Asus PVI-486SP3, PCI 486 boards are pretty much crap. Ideally what you'd want is a VL/EISA combo, but as these are hard to find, always use a DALLAS clock chip, and require EISA config files (which might be hard to locate), I would stick with ISA/VL board. There are tons of them, and they are cheap.
My two favourite types of VL boards are those based on the SiS chipsets, or the micronics boards common to the Gateway 2000 systems. Memory interleaving is a feature I wouldn't want to be without, so make sure your board supports it. Other things like support for writeback cache and 3V support are nice, but not as critical. However, if you want to use a DX/4 CPU, you'll need a separate voltage regulator if your board doesn't have one built in.
People in this forum seem to like graphics cards based on the S3 chipsets. If I were to go that route, I would probably get one based on the 805i, 864, 868, 964, 968 or TRIO64 chipset. S3 may be more compatible, but I strongly feel cards based on the Tseng ET4000/W32P chipset are a hell of a lot faster. The big problem with Tseng cards is quality. Most of them were value oriented and don't come with very good RAMDACs. Better quality boards are made by Hercules and STB.
For sound, I would prefer an SB Pro 2.0 with an LAPC-I card. MT32 cards are scarce and expensive though. Some people seem to like cards based on a certain version of the Crystal chipset that is SB Pro compatible and has a real OPL3 chip. What I'm running at the moment is an SB16 with a DBXG60 MPU-401 card. It's not a bad combo, but finding an SB16 without the hanging note bug is a real problem. DSP 4.05 seems to be the one to look for.
Hard drive performance is something that people on this site don't really seem to talk much about, but something I find critical for good performance. When possible, I always equip my systems with SCSI. The only problem is that on an ISA-VL board you don't really have a proper bus for a SCSI card. ISA is too old and doesn't provide enough bandwidth (though it's still useful for SCSI CD-ROM drives). VLB is a botched job and can't busmaster properly. The only decent SCSI cards on VL bus are the ones that have lots of cache, but these cares are few and far between. Therefore in your situation, EIDE may be the way to go. The basic EIDE VLB controllers really aren't too bad, but if possible grab a caching controller.
"Will the highways on the internets become more few?" -Gee Dubya
V'Ger XT|Upgraded AT|Ultimate 386|Super VL/EISA 486|SMP VL/EISA Pentium