I would use an Intel DX4-100 or a DX2-66 paired to a motherboard with the 420EX chipset from a reputable manufacturer. A Matrox Millennium graphics card, AWE32 (non-PNP) sound card and an SCB55 daughterboard, a TurtleBeach Multisound sound card, a 5400rpm hard drive of some sort, Windows For Workgroups paired with DOS 6.2. A CD-ROM drive of course and I'd go for the smallest case I could gracefully fit everything in; preferably under the monitor desktop style. 64mb of memory just to make sure I have plenty for use in Windows.

While it would definitely wouldn't score the highest benchmarks, I'm confident that setup, if executed right, would be at the top of the heap in terms of stability.

Of course, I think it'd be fun to also build a system using an AMD 5x86 and a VIP board of some sort; I know UMC had a chipset that could do 66mhz and supported EDO. Grab an S3 Virge or a Trio64 and either a Gravis Ultrasound or a SoundBlaster AWE32 to throw in it as well. The case would be the tallest tower I could find, have a turbo switch, LED readout, mismatched 5.25" bay cover panels and dorito/cheeto dust fingerprints all over. Windows 95B would be the OS.

The first system would be my 1994 power box, the kind you'd expect to see in the office of some company manager who talked accounting into giving him a generous budget; just shy of Sparc or Pentium generous and the second system would be my 1996 apartment-dwelling ricer box.

Some will say an overclocked Cyrix5x86.......... but wouldn't you want the best 486 possible that can still boot and use Windows 95 without crashing?

I thought my AM5x86 160MHz junker was good (59.5 speedsys score, 71.4 3dbench) but it could be better if it had a PCI Riva TNT or a PCI ViRGE...

I gotta agree with GXL750 for the most part in my moderate experience as far as stability goes. But I need to ask you; what you mean by "best"?
Fastest would be a late model PCI UMC chipset board with a Cyrix based 5x86 CPU (like my personal favs, the Shuttle HOT-433 and Biostar 8433UUD), either a Matrox, ET6000, or a Trio64 (maybe paired with a Voodoo card for those few games that could take advantage of it), 64MB 60ns RAM at 256kB cache (or if the board supports 1mB cache, 256MB).

Other details would be:
Multi-boot software with WFW 3.11, Dos 6.22, Windows 95C (was the most stable version I ever used), or perhaps Windows 98SE if you want to show off the CPU's strength. Sata or SCSI controller for HDD/Optical drives. Sound cards would be a GUS and AWE 64 Gold, maybe.

I could go on and on, but "best" is very subjective so I can't really answer much better than that with out more data.

If you're looking for the best possible 486, you might benefit from reading the Ultimate 486 Benchmark Comparison and the World's Fastest 486. Links provided below,

The Ultimate 486 Benchmark Comparison
The Ultimate 486 Benchmark Comparison
There's a much easier to read PDF at the end of the fist post.

The World's Fastest 486
The World's Fastest 486
I consider this the best compliation of hardware for a 486 system.

Some will say an overclocked Cyrix5x86.......... but wouldn't you want the best 486 possible that can still boot and use Windows 95 without crashing?

An overclocked Cyrix 5x86, say at 133 MHz (2x66 MHz), just needs a little more cooling than the average overclocked AMD. If you put the 486 motherboard into an ATX case with proper inlet/output fans, the system won't crash at all. I've run an overclocked Cyrix 5x86-120GP and IBM 5x86-100HF with the case off and an extra side fan for days without crashing... in Windows.

If your motherboard doesn't support 66 MHz operation, you can run a stock Cyrix 5x86-120 with enhancements on. This CPU will best an AMD x5-160. Please refer to Cyrix 5x86 Register Enhancements Revealed for more information on enabling the Cyrix 5x86 special enhancements.

Cyrix 5x86 Register Enhancements Revealed
Cyrix 5x86 Register Enhancements Revealed
There's also an easy to follow PDF at the end of the first post.

If your motherboard doesn't natively support a 66 MHz FSB, it is very easily possible to add a 2X multiplier between the FSB and the CPU on the CLK path. For example, with a Biostar MB8433-UUD, you can remove resistor R79 and connect a 2X PLL, such as an ICS512. They are $3 each. Here's the digikey link,
http://search.digikey.com/us/en/products/ICS5 … 44-1-ND/1916107

This operation is really a no-brainer to do and will work on just about any motherboard. So if you are running your motherboard at 33 MHz FSB, the clock sent to the CPU will be 66 MHz, but the FSB will still be at 33 MHz. This way, you don't need to mess with FSB-to-PCI clock divisors in the BIOS if your board doesn't support this. Using an IBM/Cyrix 5x86-100, you'd set the multiplier to the 2X setting to get 133 MHz. You could also run your AMD X5 at 200 MHz without using the 50 MHz FSB setting, just set your AMD X5-133 up for 3X operation (33. MHz x 2 x 3 = 200 MHz.)

With a little more effort, you can put this 2X PLL into a PGA pin adapter and re-route the CLK pin. For more flexibility, a PLL in the 1X-2X range would be preferred. The one I spec'ed (and have on hand) is for the 2X-8X range, which would be fine if we could find a way to force our CPU's into 1X mode.

Really this topic was just to fantasize your ideal 486. Some would go for all out speed, others a true period piece or something that works well with games. I just found it interesting what others would do without the limits of actually finding/paying for the stuff.
The family upgraded from an Apple IIe to a 486 DX2 66 & that’s when I became a computer nerd so the 486 has always remained my favourite

My ideal 486, if money was no object, would be what I have listed under The World's Fastest 486. Unfortunately, money has been an object, so this system has slowely progressed from Jan. 1997 until now. There's nothing I'd change, except for maybe a 3.5" external PCMCIA card reader to play with.