On that kind of budget I'd wait a couple months for SB-E. It'll be the new enthusiast platform from Intel to replace the X58/LGA 1366. You'll be able to get a top of the line motherboard and a 3930k for less than $1000. If you want the best there is right now for gaming, I'd grab a 2500k and a Z68 motherboard, I don't know which mobo is the best.
My suggestion would be to read the past few toms builds in their systembuilder marathon series. The most recommended cpu is usually the Intel i5 2500k. You don't need to spend a lot on a motherboard to operate this cpu. You will want to overclock this cpu and you will need a good aftermarket cpu cooler to go with it. You could do this for about half of your budget.
There are some motherboards that operate better with certain GPU systems so you need to decide what GPU system you want to run and then pick a motherboard that will work with it.