it does not matter, BUT, you should compare boards in the similar price range.
it would be unfair to compare say a $60 dollar matx board to a $200+ atx board, there would be a difference in perf and features there. overclocking alone should make a big deal (cheap ones tend not to have good heatsink in the mosfets for example)
but if both are similar in price, then there should be minimal. the cpu and gpu are bigger factors than mobo size.
as an example, check out asus's boards, they have matx (gene i think is one) and full size atx. gene is small but performs well (it is also expensive though) just like the bigger siblings
Lucky for me I don't really intend to use anything more than what's on a microATX mobo or overclock either. Thanks for the info!