when you overclock a motherboard, it basically means making the transfer speeds faster. the most common thing to overclock is the FSB or Front Side Bus (or if it's an Athlon 64 it would be the HTT), the link between CPU and RAM (which also overclocks the RAM)
the CPU's speed runs at the speed of the FSB multiplied by the "multiplier"
the CPU in my home computer is a Pentium 3 933MHZ
it runs at 133 (FSB) * 7 = 933MHZ
but now I have it overclocked, it is 150 (FSB) * 7 = 1050MHZ
the multiplier usually does not change. sometimes it does, but usually not.
when people overclock, often they will lower the multiplier so they can raise the FSB even more. this gives about the same core speed, but faster memory access
for example, if I lowered my multiplier to 5 on my CPU, I could raise the FSB to 210MHZ to get 1050MHZ core speed, but the memory access is faster. I can't really change my muitiplier because that's how Intel made it, but you see how it works
you choose the motherboard based on what parts you have/are getting, and on the quality. a low quality board will often make your system crash, and/or not let you overclock as far, or would have some other drawbacks
I often look at brands. if there is a brand I don't know, I find out what other people's experiences are before I buy it
some good brands are Abit, Asus, Gigabyte and DFI
99.9% of new motherboards now are standard ATX, and some are Micro ATX.
any Micro ATX board will fit in a standard ATX case, it just won't use all the peripheral card brackets at the back