Ok, so here are my 2 cents..

System I
Audio: This really depends on whether you want a single or multi card setup, and how much DOS compatibility you want. If you are going to require no DOS compatibility an Aureal Vortex 2 card is a slam dunk here, but you don't seem to have one. Of the lot you own I'd go with Terratec Fortemedia TT801-QD which has good sound quality, optical out, an acceptable OPL3 core that is very DOS compatible as well as a software synth for Win9x.
2D GPU: Steer clear of early nVidia cards, their VGA IQ is pretty bad out of the box and get even worse in a Voodoo setup. Again, if you don't want/need DOS compatibility, G450 will give you great IQ with good D3D acceleration so I would be OK with that.

System II
CPU: When you say Lucas games that covers a very wide range, and some of the later games (The Dig etc) require processors that earlier ones won't be compatible with. Personally with this system I'd go for at least a DX2-66 and disable L1 with Setmul if necessary.
Ram: 16MB should be good enough, 32MB would be nice if you want to set up a RAMDISK or something. Without knowing how much cache you have on the motherboard, don't exceed 32MB.
Graphics: Cirus Logic VLB Card will be fine
Audio: You need something with an unbugged MPU so just steer clear of the Sound Blaster 16. CT3910 has OPL3 and a working MPU401 so it's the obvious choice here.

System III
Mobo: Tekram P5T30-B4E
CPU: The 200MMX with Setmul will give you the best flexibility here
Ram: 32MB or above, max out the 64MB if possible.
Graphics: This depends on how good your S3 cards are; most have very shitty washed out and muddy output, but if you are lucky enough to have one with a sharp and strong signal then go with it. Otherwise, Matrox Millenium 2MB.
Audio: Again, the buggy MPU-401 disqualifies the SB16. If your CT3990 has an OPL3 chip, then use that, otherwise use the CT4500 AWE64.

appiah4 wrote on 2021-03-31, 09:57:

System III Mobo: Tekram P5T30-B4E CPU: The 200MMX with Setmul will give you the best flexibility here Ram: 32MB or above, max ou […]
Show full quote

System III
Mobo: Tekram P5T30-B4E
CPU: The 200MMX with Setmul will give you the best flexibility here
Ram: 32MB or above, max out the 64MB if possible.
Graphics: This depends on how good your S3 cards are; most have very shitty washed out and muddy output, but if you are lucky enough to have one with a sharp and strong signal then go with it. Otherwise, Matrox Millenium 2MB.
Audio: Again, the buggy MPU-401 disqualifies the SB16. If your CT3990 has an OPL3 chip, then use that, otherwise use the CT4500 AWE64.

See attached S3's I have. Do you think I need to put heatsink or cooler on my 486dx2-66? it gets 70-75 Degrees.

oguzog wrote on 2021-03-31, 14:35:

appiah4 wrote on 2021-03-31, 09:57:

System III Mobo: Tekram P5T30-B4E CPU: The 200MMX with Setmul will give you the best flexibility here Ram: 32MB or above, max ou […]
Show full quote

System III
Mobo: Tekram P5T30-B4E
CPU: The 200MMX with Setmul will give you the best flexibility here
Ram: 32MB or above, max out the 64MB if possible.
Graphics: This depends on how good your S3 cards are; most have very shitty washed out and muddy output, but if you are lucky enough to have one with a sharp and strong signal then go with it. Otherwise, Matrox Millenium 2MB.
Audio: Again, the buggy MPU-401 disqualifies the SB16. If your CT3990 has an OPL3 chip, then use that, otherwise use the CT4500 AWE64.

See attached S3's I have. Do you think I need to put heatsink or cooler on my 486dx2-66? it gets 70-75 Degrees.

Many DX2-66 had "Heatsink required" printed onto the top of the CPU and iirc basically all s3 systems I salvaged parts from did have a heatsink mounted on a DX2-66 (was one of the more common 486 CPUs I encountered back in the day) . I would add a heatsink to a DX2-66 (especially if it's one of the more common 5v parts).

oguzog wrote on 2021-03-31, 14:35:

See attached S3's I have. Do you think I need to put heatsink or cooler on my 486dx2-66? it gets 70-75 Degrees.

Impossible to tell S3's apart by looking at the card, would need to see it on the monitor I'm afraid.

As for your DX2 - if it's a 5V CPU it needs a cooler or at the very least a very well ventilated case. If it's a 3V CPU you can get away without one even in a cramped case.

Using a cooler will help with giving the part a longer life in all cases.