I doubt you can find one that is micro ATX and does NOT have onboard video. It seems not to be possible.
Either way here's my recommendation:
Get an intel chipset, not nvidia for sure, because it doesn't always work.
Check the HCL:
http://www.linuxquestions.org/hcl/index.php/cat/8
As well as:
http://hardware4linux.info/
I've used ASUS, Gigabyte, and Intel motherboards and I've had the most problems with Gigabyte, and the least with Intel. I wanted to try Abit, but it just wasn't available.