Arrested Development - i think the humor of this show escaped some people.
Freaks and Geeks - to PP, I think they originally had a different idea on how the episodes would air, but when they knew they were getting cancelled they had to rearrange the order they aired because it wouldn't end right. The network they were on (I forget which one, because I watched it on DVD) kept telling them they had to reshoot certain scenes as well because they were too racy for a high school show. I think a lot of the content in the later episodes was sacrificed in an attempt to keep the show on the air.
Alias
Veronica Mars - i dont think this show was given a chance either. i just wish it had a more definitive ending. :( i <3 logan echolls!