Here are my guidlines when I am going to buy motherboard and start choosing what motherboard I will buy. 

Decide which CPU to use
Buy a motherboard that uses the right chipset
For a single Pentium 4 or Celeron processor, choose a motherboard that uses an Intel 845-, 865-, or 875-series chipset, depending on your budget and priorities. For a single Athlon processor, choose a motherboard that uses an nVIDIA nForce2-series chipset. For a dual-processor Athlon MP system, choose a motherboard that uses the AMD 760-MPX chipset.

Make sure the motherboard supports the exact processor you plan to use
Choose a board with flexible host bus speeds
Avoid hybrid motherboards
Check documentation, support, and updates
Buy a motherboard with the proper form factor

CHARACTERISTICS

Expansion slots
Warranty
Ports, connectors, and front-panel LEDs
Embedded sound and video
Power management and system management
Wakeup functions
Jumperless (or single-jumper) configuration
Boot devices supported
Minor or special-purpose features