here are my preferences. i have personal experience with all of these brands:
Abit: my personal favorite. the OCers favorite--my KT7A pushed my duron 600 to 1 GHz and i will not forget it =) well built, good 3 phase power, tend to be pricey
Asus: well built boards. tend to be pricey and sometimes have quirky features, but overall a great pick when you want good stability and some decent overclocking. their Asrock division is trying to make discount boards to compete against ECS.
ECS: best bang for the buck. cheap boards and generally stable as long as running in spec. can have some quirks in stability, but if you know what you are doing, they are darlings. not a board for a first-time builder--the infamous K7S5A can be a heartache for many.
MSI: i despise them. tend to rush to market without fixing bugs. generally not 3 phase power. flashy boards with poor performance. they are a very big OEM maker for HP, Dell and other builders, but they do not make good enthusiast boards.
Epox: good stuff here. OC friendly, their port 80 display is a godsend for POST problems. good performance, good 3 phase power design. highly recommended with Asus and Abit.
Soyo: a pretender like MSI. in general, they make flashy boards that are buggy with less than top-of-the-line performance. tend to be pricey too. stay away from them.
Gigabyte: good stuff here. dual BIOS is something that more mobo co.s should use. stable, well built, good innovation. a good choice.
Shuttle: had one shuttle board fail, but all of my SSF comps run great. well-built, not particularly OC rich but they are OC friendly. their SSFs are the best in the biz though.
Via: all of my Eden systems run great. stable, small, and pricey. i have not tried any of their VPSD boards though, but i would assume they are good build quality too.
Intel: no personal knowledge, but well renowned for their stability, but not their overclocking or speed. i have yet to hear a negative comment about stability so i have no doubts here.
there are other companies, like Biostar, Albatron, Supermicro, Tyan, etc. i do not have any personal knowledge of these companies, so i don't want to say anything. my picks for boards are Abit, Epox, Asus, Gigabyte in that order.