I'm a very practical person,
I'm a big fan of

Avoid STD bus.
It's very Z80-oriented, so non-Z80 designs have a harder time of it.
The bus connector is card edge.
These are fine on the desktop, less so in other environments.

STEbus is much smarter than STDbus.
The bus signals are very simple and sensible.
Like an 8-bit VMEbus. It's easy to make various processors
fit STEbus.
The board size is 100x160mm Eurocard.
Thus it fits in off-the shelf Euroracks.
The edge connector is 2x32 way DIN41612.
Thus the prototyping  boards  are cheap and connectors
easily available.
Arcom Control Systems in Cambridge UK have a wide range of
STEbus kit. Major catalogues like RS and Farnell chose to
supply their kit - take a look.

PC104 is very dominant because the connection system
means you don't have to buy a costly backplane, and
although not as reliable as STEbus, it is more reliable
than edge-connectors. Thus it is reliable enough for most people.
It uses PC signals and chips, so cost benefits from this mass market.
Mechanically they're pretty poorly thought out.
Being so small, CPU boards are pushed for surface area.
Connector space is very limited, so cabling gets untidy quickly!
Pins are prone to bending. Cooling can be a bugger.

Arcam do CPU boards that are Eurocard size for easy rack mounting,
and use a PC104 bus so you can plug cheap PC104 boards in them.
http://www.arcom.co.uk

If you want PC104 sized boards, I can recommend DSP Designs.
I've always had good service from them. Even though I said
up front I was only likely to buy one or two, they were kind
enough to visit. They're in the UK for local service.
http://www.dspdesign.co.uk

Compact PCI is nice: Eurocard sized, DIN41612 connector,
AND PC-technology chips. PCI chips are not yet as cheap and
easy to design with as PC ISA chips, and embedded systems
don't often demand the extra performance.
I hope it grows its market share.

The DIMM-PC is a 386+FDC+LPT+2xCOM at TTL in a DIMM package!
See JumpTec in Germany at http://www.jumptec.de
0.8mm pin spacing means you can't lash up a prototype on
0.1" protoboard, but this may not be a problem to you.