Acer, Dell, and HP.... Avoid at all costs. Even if you're just trying to score an "ok" GPU, they usually ship with a custom model that has that manufacturers specific ROM dragging it down. (Also may or may not have adequate cooling)
I've had good luck with CyberPower and CUK (Computer Upgrade King). You are usually going to get a good value there, and they build quality systems. iBuyPower used to be good, but their quality control has been dropping lately. Still a good choice if you're mostly looking for components though.
You can also take the route of build-to-order systems like NZXT, Build Redux, Digital Storm, or Origin. (There are probably others. This is just want I could think of off the top of my head.)
Jayz did a vid on things to check/avoid recently as well.