The first thing is to bay a good brand (ASUS, GIGABYTE, EVGA,...)
After that:
- Good chipset (and good manufacturer, of course)
- Type of RAM supported
- Good on-board layout for expansion slots, SATA ports (RAID support), power connectors, fan connectors,...
- Availability of processors (cpu socket)
- Good refrigeration system (northbridge, southbridge, VRM,...)
- Only solid state capacitors for longer life time and better reliability
- Powerful BIOS features, such as: Ability to tweak memory timings, base clock, multiplier, large voltage adjustment range with small and accurate increments, high number of sensor readings, BIOS backup feature and support for saving multiple BIOS profiles, ...
- Good backside IO ports (USB, FW, eSATA, network, ps2 ports, ...)
- Good on-board sound/video chipset and output, unless you use separate expansion sound/video card.
- Good warranty (length and quality of service)
- ...