Nah, those aren't stupid questions. We all started out in the same boat as you, not knowing much

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quote redneonfish
I know there are two main types of motherboard, AMD and Intel. Both motherboards can support Nvidia and ATI gpus right? The only difference is which cpus they support?
For the most part, thats correct. As long as the motherboard has a
PCIe x16 port, it will support the majority of new graphics cards.
quote redneonfish
And what do are 'sockets'? For example, a motherboard can take a 1366 cpu? Does that refer to the size of the cpu or something?
A socket is how the CPU plugs into the motherboard. There are many different socket types. A socket LGA 1366 will only be compatible with a socket LGA 1366 CPU (in this case it would be an Intel core i7). An intel processor with a socket LGA 1156 will not work on a motherboard that has a socket LGA 1366.
AMD processors work in a similar way; a socket AM3 processor will work on a motherboard that supports socket AM3.
The socket is just a way of saying how many pins and what size a processor is and helps to figure out what processor will work on a motherboard.
This is the socket 1366 on a motherboard and
this is a socket 1366 processor.
quote redneonfish
Also, which brands would you recommend for a new motherboard?
I like Asus, Gigabyte, MSI and EVGA. Those are generally all good manufactures and the first ones I look at when shopping for a new motherboard.