After watching a few more episodes from season 7 of The Simpsons on DVD, I'm now completely certain that Fox edits at least some of the episodes down about thirty seconds or so for syndication. It seems that every episode I watch reveals a few short scenes that I've never seen before, and I've watched these episodes a lot of times. I'm not talking about the mostly-bad little deleted scenes that are clearly marked as deleted scenes that you have to press Enter to see and don't even always have the correct actors providing the voices; I'm talking about a few seconds here or there at the end of a longer scene, or maybe something that was maybe a little too racy for afternoon TV.
My favorite scene that I never saw before the DVD is from "I Love Lisa" in season 4, the "I choo-choo-choose you" one with Ralph and Lisa:
(on the way to Krusty's 29th Anniversary Special)
Lisa: Chief Wiggum, how did you ever get these tickets?
Chief Wiggum: Krusty knows how to play ball.
(scene switches to porno theatre)
Chief Wiggum: Ah… nothing beats a good porno movie.
Krusty: Chief Wiggum! Is this a bust?
Chief Wiggum: Uh, yeah! That's just what it is. A bust.
(scene switches back to police car)
Lisa: That story isn’t suitable for children.
Chief Wiggum: Really? I keep my pants on in this version.
I saw that episode about ten times on TV before DVD, and I never saw that scene. Back then, I thought that scene was an anomaly, and given its setting, I could see why it was edited for TV. But, so many things in season 7 that I'd never seen before were perfectly fine and didn't need to be cut for content.
Fun fact from Wikipedia: Al Jean's wife had "I choo-choo-choose you" engraved on his wedding band.