The 486 PC was quite for a long time on the market.
Although being first introduced in 1989, most people probably hang onto their 386 PC's until at least 1992, after which the prices of the CPUs started to come down due to competition from AMD & Cyrix.
I think the first thing you need to ask yourself is whether you want a motherboard with VESA Local Bus slots or PCI slots (or a combination of both).
Although the 486 started out on only the ISA bus, it would be sub-optimal to run a 486DX2 66 MHz or faster on an ISA only graphics card.
Some people firmly believe that a 486 CPU should only be paired with a motherboard that has VESA Local Bus slots (since this was specifically developed to cater for the 486 architecture).
One of my favourite 486 VESA Local Bus motherboards is the Asus VL/I-486SV2GX4 and utilises the SIS 471 chipset. What I also like about this particular Asus motherboard (and most of their later 486 motherboards) is that, unlike most other 486 motherboards from other manufacturers, this one also has a PS/2 header on the motherboard.
The SIS 496/497 chipsets (that you also referred to) was mostly used (from what I've seen) on PCI based 486 motherboards. Although, they were also used on ISA/VESA Local Bus/PCI combo motherboards as well (the Asus PVI-486SP3 being one example). Other PCI based 486 motherboards that I found to work quite well is the Luckystar LS-486E motherboard (utilising the SIS 496/497 chipset) and also the Gigabyte GA-5486AL (utilising the ALI M1489/M1487 chipsets).
There are pros and cons to each one but, in the end, I think your biggest deciding factor will be availability and price (since 486 motherboards are becoming more scarce and pricey).
PCI based 486 motherboards were introduced quite later on so that, by that time, the technology had matured already to a point where you had much more stable motherboards and, in most cases, on-board IDE, floppy, serial & parallel connections (as opposed to VESA Local Bus motherboards, where you, in most cases, required an IDE I/O controller card as well). SCSI was also an option on both of these but, normally via an interface card.
Most PCI based motherboards also had greater support for later 486 CPU's (specifically, the 3.3V DX4 100 MHz and faster CPU's including the Cyrix 5x86 & AMD 5x86 range of CPU's). Earlier motherboards either required a BIOS update (via a physical replacement of the BIOS chip) or, didn't support those at all (due to either no updated BIOS being available and/or no voltage regulator for the later 3.3V CPU's).
