You're pretty much bound to find Foxconn components on just about anything including ASUS motherboards. They also make intel and apple mobos. They are not really so much an underdog. Everyone I know who has had a branded foxconn board has hated it however.
I've always been partial to ASUS, Gigabyte and MSI desktop motherboards. MSI only for its usually really good overclocking abilities. I don't really know too much about server boards except Tyan and Supermicro seem to do fairly well in that area.
Also yes, Supermicro designs desktop and server boards but mostly they just focus on the server market AFAIK.
Edit: Even though you said you weren't looking for an ASUS. If you're looking for an mATX, you should check out ASRock boards, ASUS' little cousin but less in price and supposed to be more stable. Good luck with whatever you decide, hope it works out for you!