On the DVD version of the episode "When You Wish Upon a Weinstein", there is an alternate line in Peter's "I Need a Jew" song. The Cartoon Network/Fox/TBS line has been changed from "Even though they killed my Lord" (The Original and DVD lyric) to "I don't think they killed my Lord." If you look closely, you can see Peter's mouth reading the original line.
The commentary for "Road To Germany" has been cut in the UK by 46 secs by the BBFC to remove very strong language. Fox were offered an uncut 18 certificate but declined.
Some episodes air in a somewhat-edited version in their original FOX airings and syndicated airings, but air in a racier, "uncut" version on Adult Swim, with some extra scenes or alternate versions of scenes. However, Adult Swim still bleeps the most profane of language.
Versions of the show that air in syndication often have their commercial breaks in different places than the original network airings. This results in some rather jarring transitions that were not present in the original broadcasts, and commercials in strangely inappropriate places. One good example of this is that Peter introduced the cutaway about a secret place for his porn, then it went commercial, and the cutaway did not play until after the commercial break!
Germany had the episode where Peter takes over for the Grim Reaper cut because one part had a scene where the Grim Reaper tells Peter over the phone about how bad the world would be if there was no death. The Grim Reaper then adds, "Imagine a world where Hitler was still alive" and the phone conversation cuts to a talk show called, "Hitler".
In the DVD and Cartoon network version "Brian Wallows and Peter's Swallows" during the Musical montage there was a small shot of the World Trade Center and when Brian is showing the woman Tarot cards Originally had President Bush holding a beer funnel on the last card of how the world will end. The FOX version cut the World Trade Center and changed the Bush tarot card to a Jerry Springer Card
Episode 2ACX12, "Road To Rhode Island" had a scene cut from its DVD and syndication versions post 9-11. Originally, Stewie distracts the guards at the security checkpoint so they don't look at the contents (guns, granades) of his bag as it gets X-rayed. After he gets away with it, he quips, "I hope Osama bin Laden doesn't know show tunes." This was followed by bin Laden fooling the guards in a similar manner while singing "God I Hope I Get It" from "A Chorus Line."
On the "Freakin' Sweet Collection" DVD, the Osama Bin Laden scene from "Road to Rhode Island" has been restored.
Adult Swim added a joke that wasn't on the network airing and had a theme song for the episode "Breaking Out Is Hard To Do".