I have a very hard time thinking of many bad episodes from the FOX seasons. The closest I can think of are "That's Lobstertainment" and "Bender Shouldn't Be Allowed on TV", and that's mainly because they're just pretty bland and really just bumps in an amazingly consistent 4 seasons.
Out of the movies, "Bender's Big Score" was clearly the best. But IMHO they really blew everything that had with that one. "Beast With a Billion Backs" and "Into the Wild Green Yonder" were mediocre, while "Bender's Game" was great until it got to the played out Lord of the Rings parody, where it stumbled badly. As I said in another thread, the staff of this show knows their main audience is the same group who has stuck with the show since the very beginning. So they don't have to try very hard as long as they throw favorite characters in fan's faces and and continue to bring back elements such as the Globetrotters, Santabot, the Robot Devil and (ugh) Barbados Slim.
This is why we're at the point where "Manwich!!" and Scruffy - things that were funny every so often - are used all the time now. Scruffy is no longer funny because he's in every episode. But that hardcore Futurama fanbase seems to love him, so there he is. What do I know.
Then we come to the Comedy Central episodes. Yes, there are some good ones, but like South Park it's become a crap shoot on whether or not you'll get one. Out of the last 4 episodes that have aired, I've only thought "Benderama" was any good, with the Xmas special being the worst half hour of Futurama I've ever seen. Unfortunately the show is heavily relying on topical jokes, gross-out humor and juvenile sexual jokes, I suppose in order to win over the immature casual Comedy Central audience who would otherwise not watch this show. Yes, this sort of stuff appeared in the FOX episodes, but here the knob has been turned up to 11.