I would recommend using a 486 desktop for dos, just avoid those old VLB cards if possible and NEVER use VLB cards for your video and hard drives. Get a real soundblaster card and some floppy drives, windows 3.1 helps for configuration because too, If you need CD-ROM stuff avoid SCSI unless your hard drives are also SCSI or your sound card forces you to do it, Also try to get one that is configurable and have a few different CPUs to go with it.
I would recommend a dual boot 98SE and XP machine for most games from 1995 -2002, get an old PIII tualatin based server for this, preferably one with easy access ram slots and don't use a HDD bigger than 60gb for the 98 side. Make sure you inspect the motherboard for bad caps!!!
Use a modern Gaming PC with Win7 and XP mode for everything after that.