I've been moving towards a good old DOS setup, and I'd love to get a '386 setup in a non-traditional box, like retrofitted into a classic console or something.
I think the big dividing lines are pre-640K and post-640K, as well as pre-USB and post-USB.
Dealing with expanded and extended memory was very case by case for software, so it is a bit of a pain.
Everything before USB is a bit of a pain to deal with for any expansion. The thought of dealing with Com ports and IRQs sends me into convulsions. It sucked then and I can't imagine it would be better now.
I have a working Tandy 1000EX but I'd like a regular 1000 setup for use. I have a Tandy 1000 that has issues I've been meaning to troubleshoot, but no time. Been meaning to post a pic of the boot screen on one of the more Tandy oriented boards.
For building a retro PC, the big dividing lines are operating system (software) and system bus interface (hardware).
While the line of what counts as "retro" is slowly moving, most people think about the DOS era through the Windows 98SE era (very similar to what counts as "retro" with console gaming). For the most part, the two operating systems that really matter are DOS and Windows 98SE. I believe there are some Windows 3.0/3.1/95 games that don't play well with Win98SE, but they're not deal-breakers. In fact, DOS was still the platform of choice for big-title developers well after the debut of Windows 95: Quake (1996), Duke Nukem 3D (1996), and Blood (1997). So, if you get a rig that can run Win98SE well (Pentium II at least), you can play most of the best games of the 1995-2000 era, as well as some earlier DOS games (you'll need to slow down the system for really early stuff by turning off the caches or using a slowdown TSR).
The system bus interface matters because you want an ISA slot, preferably two or three. The only P4 motherboards that include an ISA slot are industrial (and expensive), and some of those don't work right. So, your choice of processor is pretty much capped at the PIII. The most powerful retro CPU is the 1.4 GHz PIII Tualatin, with the 133 MHz system bus. It is faster than many early P4s. You want an ISA bus because you want to be able to have true Soundblaster compatibility in DOS. PCI sound cards simply aren't great in DOS, although some are okay. In fact, now that my sealed Intellivision collecting has hit a wall, I find that I'm collecting rare ISA sound cards.
The good news about retro PC gaming is that almost any problem can be solved with the knowledge available online (vogons.org is the gold standard). If you remember the bad old days of strugging with IRQs and DMAs, then know that getting a rig to work these days is much simpler because there are more resources at your disposal.