Resources for IBM PC compatible motherboard / Intel 80486 development
You basically have two options here:


A current-generation 486-based CPU

Upside:

Everything will likely be integrated into the main CPU - No southbridge, IO controllers, etc...
you can actually buy the ICs off the shelf.

Downside:

Devices may be BGA
few exposed busses
may want to run at a few hundred Mhz.

By "Currently Produced", I mean something like a AMD Geode, or similar device from VIA, etc... There is a pretty big market for small, low power, low speed x86 CPUs in embedded applications.

A old-stock or old-design 386/486 CPU

Upside:

Probably more educational

Downsides:

Requires a LOT of devices (e.g. Southbridge, a UART, etc...), all of which are additional ICs. 
Note: the external devices will vary depending on which 386/486 you decide on. The early ones had few integrated peripherals. Later on, many of the peripherals got integrated into the CPU itself.




There are some midpoint-devices, like the 386EX, which is a 386 intended for embedded applications. It's old enough that it's available in TQFP-144 (released in 1994), yet it includes most of the necessary peripherals on-die.
Datasheet



Some resources, off the top of my head:

CoreBoot:

A FOSS BIOS alternative.

Interesting forum thread about building a IBM XT compatible computer.



Other stuff:

Dieter's Homepage
Some nutjob who build a discrete Transistor CPU!
He also has a bunch of other homemade CPU projects



Really, If I were you, I would go with an ARM device. You can get big ARM CPUs that have MMUs, and will run linux fine. 

Alternatively, an 8088 or 8086 may be significantly more approachable. There is lots of information about people homebrewing 8088 computers out there.