I like both of these shows, odd that they're matched up here considering they air right after one another on the same channel every Monday night. How I Met Your Mother is going to be getting the vote from me here, and that's simply based off of my love for NPH but even moreso my love for Jason Segel, who is pure gold in everything he takes part in. As a big time fan of Freaks & Geeks, the show that gave he and so many others currently dominating comedy films in America their start, this was a simple choice for me.
I do like The Big Bang Theory (oh the things I"d do to Penny!), but HIMYM is getting my vote here. Not as great as some people make it out to be, but still a very good show.