The board qualities do vary even within the same brand, it's somewhat affected by their quality control standard and testing, which means flagship products should be better on average if you have a sample of 1000 units, but those tests and components also make them more expensive. But for the most part, it's really like playing lottery, it's all pure luck when you're just buying 1 or 2 boards for personal use.
Personally I've used Asus, Gigabyte, ASRock, Foxconn, Abit, Biostar, Elite group (ECS), Chaintech, EPoX, and First Int'l (FIC), to build for family and friends. It's kind of funny now that I think about it. I've never bought a brand twice!! I always went after price at the time.
Foxconn for Core2Duo was DOA and was returned, and I just never warmed up to it since then.
EPoX with Athlon was affected by capacitor plaque and blew its caps after 4 years.
Abit with Core2Duo was somewhat fussy, required a lot of tweaking in an overclocked system, still working fine after 3 years.
Chaintech with Penitum4 been very stable by comparison and still running strong after 6 years.
Both FIC and ECS are the cheapest of the cheap boards, but performed really well (but I never overclock those). I could still boot up my Pentium II LX440 board after 13 years.
The ASRock with AthlonXP after 4 years recently had issues with random shutdowns and USB detection. I haven't had time to deal with it enough to know what's going on, probably a board issue though.
Biostar with Athlon II X2 is a recent buy (replaced ASRock system above). BIOS was limited but it was a no-frill budget board, once I had it set correctly, it's been stable after 4 months.
Best of the bunch? My Asus with Core2Quad and Gigabyte with Athlon II X4, but Asus is only 2 years old, and Gigabyte is just 2 months old. Both are really excellent though, clean BIOS, highly stable, and well designed with connector placement. But those are also more pricey boards since I built them to my own spec. If I have to buy again tomorrow and for best quality, it'd be between those 2 brands and whoever has better price wins.