The last half-hour or so of 
Battlestar Galactica was virtually the only weak point of the show, apart from the episode "The Woman King". A special demerit to 
FlashForward's for not resolving anything, although that's the fault of the show getting (warning: tvtropes link) 
Screwed by the Network and not the writers' fault. I'm still bitter about that. It would've been an awesome season finale, too, because it was obvious they were setting up a bunch of teasers for the next season in the last few minutes with 
(SPOILER)the second flashforward, but as a series finale it was just dire.
As for good series finales, 
Arrested Development and 
Lost are probably the most memorable. I remember liking 
The West Wing's a lot too. Oh, and 
Star Trek: TNG.