VLB performance should not be underestimated. After all it was a much simpler bus and it had direct access to 486 memory bus.
Rather than performance which should be similar, I would consider whether you will be taking advantage of:
- PCI IRQ sharing - allows to install more expansion cards
- larger selection of PCI expansion cards which are newer and have more memory. You could use a 3D graphics card in 486.
- the board will likely come with AWARD BIOS which supports larger drives than those old non-LBA AMI BIOSes
- PCI PnP (not a big advantage in my opinion)
I would also vouch for PS/2 mouse connector due to ability to use optical mouse.
If you would benefit from the above advantages then I would pick PCI board even if it had slightly worse performance than VLB board.
Pentium III 900E, ECS P6BXT-A+, 384MB RAM, NVIDIA GeForce FX 5600 128MB, Voodoo 2 12MB, 80GB HDD, Yamaha SM718 ISA, 19" AOC 9GlrA
Athlon 64 3400+, MSI K8T Neo V, 1GB RAM, NVIDIA GeForce 7600GT 512MB, 250GB HDD, Sound Blaster Audigy 2 ZS