Well OhNoo, you probably will get a lot of feedback here. There are a lot of guys, including me, that build our own systems and would not even think of purchasing an OEM built computer.
If you are talking about an Intel processor, I lean towards the ASUS P4B266 motherboard. I have been using it under both Windows 2000 and XP without a hitch, save one problem.
Under W2K, the onboad C-Media sound chip is a problem. The latest drivers from MS cause random crashes when running any DX based game (DX8.1 by the way). I put in a SBLive and all is right with the world.
Again, for Intel. the socket type you look for is the 478 pin socket, which is the newer P4 design. Also make sure the motherboard supports the new Northwood P4 (13 micron) chip. This will probably be replacing the current P4 design.
The other limitation of the design is the lack of an AGP Pro slot. It only has a regulat AGP slot, but wil run AGP4X speed without any problems (at lease with an ATI8500 it is no problem).
With this motherboard, you will want 2 sticks of 256MB rame, and not one stick of 512MB ram to allow the memory controller to use the interleave memory access scheme which gives you a bit more performance. Oh, DDR or SDRAM, you want to get that from Crucial. Do not skimp on the RAM. Crucial is about the best there is on the market.
Hope that helps.