i generally am ok with foxconn , ecs, or asrock. zotac seems to be a real up and comer, especially in itx (since they are basically the only one who makes reasonably cheap boards, but they also only realy do nvidia chipsets so clearly its really only good for nvidia based baords)
THey have enough features, and are really inexpensive. Most boards are manufactured at basically the same type of facilities these days, so I don't think there is a huge difference in quality. But I personally dont think its worth it to pay extra for a company like say Asus for their reputation.
I suppose some board manufacturers have easy to use bios update tools (intel's retail boards for example), which is somewhat convenient, but it is getting to tht epoint that everyone has that too.