For the most part, the boards are all made by the same company. Between brands, there may be some variation in clock speeds and many will offer OCed versions of there cards.
Probably the biggest difference is going to be in the services and warranty they offer on there cards. Most people will tell you that XFX and EVGA are the guys to go with.
XFX offers a double lifetime warranty (incase you sell your card) which even covers overclocking and also offers great technical support.
EVGA is very similar but only offers a lifetime warranty, however they have a stepup program which in the 90 days after your purchase you may step up to a better card by paying the difference (MSRP price).
Aside from that companies will offer different buddles and packages.