As you pointed out, it's hard to find one PC that can play all of these old games well.
But you might want to consider narrowing down what exactly you want to play. Here's why: most of these games are very successfully emulated or ported.
Modern Emulation
Jazz Jackrabbit 1 can be emulated pretty well in DOS emulators, and Jazz Jackrabbit 2 is available commercially with modern fixes for modern computers.
Point+Click adventure games can usually be run perfectly in the ScummVM port.
Master of Orion 1 should run fine in DOS emulators.
Duke Nukem 3D has the excellent eDuke32 port, and many modernizations available. Terminal Velocity can be emulated. Descent has emulation and probably ports.
What to build?
So if you are going to build a PC to run old games, I think you would be best served by building a PC that runs those very few games that are hard to run at present.
There are two types of games that may be hard to run perfectly at present. The first are advanced DOS games like System Shock 1 and Fallout 1 [which had a DOS port!]. Some of the DOS games that called upon special memory functions can be tricky to emulate. Plus, some don't run quite right even today.
And what about TIE Fighter? Many ports / rereleases of that game changed the graphics, or lack essential features like the iMUSE engine. So build a 486 that can preserve that.
So, similar to suggestions on this thread, you might want to build something equivalent to a juiced 486 dx with 8 MB of RAM plus extended memory, CD-ROM drive, and all that.
I was lucky enough that my old Windows XP computer with a 4:3 LCD could somehow run System Shock [CD Edition] in XP's DOS mode. But if you want a pure experience with this stuff, you need something like a powerful 486 or an early Pentium I.
The other type, as you pointed out, are the early Windows games. With the early Voodoo cards that were so essential, and probably difficult to emulate today. [Seriously, we need a Windows 95/98 emulator with fake Voodoo support]. You could probably get away with a 233 MHZ-era build.
Then, you could play gems like "Hardwar" which is difficult to find, never mind run properly, on a modern computer. And SimCopter. And "The Sims (1)," the good one!
Master of Orion 2 is actually difficult to run today. There's a somewhat clunky DOS version [you have to emulate it], and a nicer [IMHO] Windows 95 version. Would a retro Win 95/98 build be perfect for this?
If you want to play authentic DOS Quake, or WinQuake [which doesn't run on many modern builds], this should work, right?
And, let's be honest, it would probably be just fine for the advanced DOS games that can be hard to emulate. You can use moslo programs if needed.
So, maybe just focus on those few games and experiences that are hard to reproduce today, and try to build for that, instead of a PC that handles a wide gamut of games? Maybe a 233 MHz with a Voodoo card, some kind of widely compatible sound card, and Windows 98 would suffice for everything?
Build 2 with networking, and you can have real Doom deathmatch, Warcraft 2 probably, etc... Imagine bringing back Jagged Alliance: Deadly Games multiplayer. Master of Orion 2!
