Yes, there are different types of motherboards (called chipsets. AMD, Nvidia and Intel each have their own chipsets) and then different brands. Many brands (ASUS, MSI etc.) will make their own model, based on a certain chipset.
You're right, the motherboard is the most important choice, but what motherboard you choose will depend on what you want to plug into it.
If you mean an intel Core2Quad, then you're looking at these chipsets: P35, P45, X38, X48, 750i, 780i, 790i. I'm sure there's more, but they spring to mind. The 750i etc. are SLI ones (2 or more Nvidia cards) so they're no use to you with an ATI card.
That leaves you with the P35, P45, X38 or X48 (both Intel chipsets). The newer X48 has DDR3 versions, which is the type of RAM. DDR3 is a little better than DDR2 RAM, but also a little more expensive.
The new Intels are the i7s which require a different motherboard chipset again, the X58. These also require DDR3 RAM.
Here's a quick discussion about it:
http://forums.techguy.org/hardware/8...eproofing.html
Post a specific question and I'm sure someone will get back to you