For the PCI system the DX2/66 is pretty good as its THE 486
Another option is a Pentium overdrive as gbeirn mentioned which I think is a good match for a PCI based system.
RAM: 16MB or more
Video: I'd also go with a S3 Virge, What I did was play around with S3D in a Pentium class PC but one that novelty wears off it makes a really good dos card in a slower system.
Sound: AWE64, most games will support SB16 or even the AWE natively, Adlib/OPL isn't a priority for this build.
OS: Win95, but setup so you can drop back to pure dos.
This PC will be good for later dos games and some of the earlier SVGA games, around Duke3d era things will start to struggle but are playable.
For the ISA system
Slow CPU like a 25 or 33Mhz. Intel or AMD, doesn't matter
RAM: 4-8MB is enough
Video: Something with good VGA compatibility, too many to list but once you find something ask here and we'll list its pro's and cons
Sound: SB Pro or clone such as the Yamaha YMF, OPL/Adlib IS important for this PC and most games will only support SB Pro anyway
OS: Dos, and if you want Win3x
This PC is your early 90's PC, it wont play all your speed sensitive games, but fair few broke around the 66 mark.
For both systems storage wise I would go with a Gotek Floppy emulator, and SD or CF to IDE converter for the HDD makes moving files around easy.
DVD or CD drive doesn't really matter, just whatever you already have or suits your case better. Really it'll just be used as a CD drive in either case.
Case whatever you can get. AT cases are hard to get. some people prefer traditional beige, other prefer newer cases with better airflow which are usually black. Comes down to what's available and personal preference.
I would just go with modern PSU, Sound Blaster 2.0 and even more rare Roland cards require the -5v so doubt you'll have any trouble using a nice new power supply with an adaptor.