Speaking of, the alternate ending to Clerks was much more fitting if not infinitely more depressing.
One deleted scene in Driven shows a bit of Tanto’s (Stallone) daily routine before he gets the call to get back behind the wheel. The whole thing is very reminicient of the opening of Firefox in which we see Eastwood’s character being recruited to get back in the cockpit.
I love those outtakes! Especially the ‘na-na-na-na-na-na-na-na Batman!’ on the last DVD.
A Bug’s Life had clever “outtakes”.
In Fight Club, Helena Bonham Carter is just finished having sex with Brad Pitt. She screams: “I want to have your abortion.” A great line in of itself. Apparently, the censors were distressed with it, and wanted Fincher to change it. Fincher, the artist he is, eventually relented to the studio’s request, against his better judgement. In the outtakes, HBC now says, "I haven’t been fucked like that since grade school."The studio begged for reinstatement of the original line. 
You got that backwards. The line left in was the “grade school” comment. The alternate unused scene is the "abortion"comment.
I love outtakes from any Jackie Chan movie. That guy is amazing. I also liked the karaoke scene at the end of Shrek.
Dogma: Jay and Silent Bob singing Fat Albert.
Volume 1 of Princess Tutu has some great outtakes from the English dub. One involves the voice actor for Duck quacking into her line, then when the duck on the screen stops running around, “God bless America.” A second one between the female leads–“Are you looking for something?” “Yeah, I need your boyfriend.” (Actually what she’s looking for, but not the proper line :))
But my favorite one makes fun of the pseudo-romanticism between two of the male characters. I’ll just quote it rather than explain.
“Princess Tutu. She touched me.”
“The same place I touched you? That bitch.”
What makes this even funnier is that Helena Bonham-Carter didn’t get the joke at all - she’s British and had no idea what “grade school” meant. She says on the commentary that she assumed it was high school, and it wasn’t til she heard people laughing at the line that she thought to ask.
As hinted at earlier, the deleted scenes from Best in Show are hilaaaarious.
As unhinted at earlier, so are the deleted scenes from Dodgeball.
The Terminator DVD has a deleted scene I really like. I can understand why it was taken out – the movie is an action movie with a relentless pace, and the scene would have brought it to a halt. But it’s a good scene, and pure traditional science fiction.
In it, Sarah Connor and Kyle Reese, out in the California countryside, have an argument about what to do which is based on two different concepts of time travel. Reese believes that the future is set in stone, and all they can do is try to ensure that Sarah survives to be the mother of John Connor. Sarah, on the other hand, believes that if it’s necessary for them to prevent the Terminator from changing history, that means they can change history on their own and keep the nuclear war from happening by preventing the construction of Skynet.
This reflects a theme explored in tons of science fiction stories since the '40s, and one that (if you forget about all the overblown action sequences for a moment) dominates the trilogy of Terminator movies.
Also in the scene, Reese becomes overwhelmed by his surroundings: grass, flowers, a flowing stream, clear blue sky – all things he never saw growing up in the nightmarish post-apocalpytic world of the future. He starts crying, and says, “This is too beautiful. I’m not supposed to see this.” Actually quite touching.
“Love, Actually” had a number of very good outtakes. Unfortunately, in a movie that long, something (in this case, a lot of somethings) had to go.
My favorite deleted portion involved Liam Neeson as a new widower with a young stepson. He’s surfing the internet for porn, and finds that his screen is frozen up, while filled with obscene images he can’t get rid of. At that moment, his stepson’s grandfather stops by for a visit, eager to show Liam a new golf site he’s found on the web.
Grandpa immediately goes to Liam’s computer and sees all the obscene stuff. Liam pretends to be shocked, and runs to his stepson saying, “I’ll give you 100 pounds, if you’ll just agree to everything I say.” The kid takes the rap for looking at the dirty web sites… and whereas Grandpa would’ve been furious at Liam, he takes a relaxed, “Well, boys will be boys” attitude when he’s convinced his young grandson was the lecher!
Not sure if this counts, but Tenacious D’s DVD has some great stuff on their “on the road” documentary. The scene with Lee doing the XXX rated version of “9 to 5” had me rolling.
My favorite deleted scene is still the French Nightclub scene in Singles.
Back to the Future: Marty dressed as a Hispanic homeboy – hairnet, wifebeater, etc. – watching his teenage mother cheat on a test:
<Cheech Marin voice>
The bitch is CHEATING, man!
</CMv>
I always thought she was doing a scene from Flowers in the Attic. From one of the novels not from the movie version which is infinitely funnier.
My favorite cut scene from Best in Show is the one where Guest as Harlan Pepper is showing the camera his other hobby and he opens a door to a large barn and beachballs spill out. There’s this moment where it looks clearly that Guest as an actor didn’t know what would be behind the door and is surprised and then continues and explains why he has a beachball collection. I always assumed they (Guest and Levy) came up with that bit and Guest told Levy to surprise him.
For the best outtakes and bloopers, you have to go way back- any Burt Reynolds film from the late 70’s and 80’s will have you laughing your ass off! Burt & company were just hilarious people who couldn’t help but crack each other up. He & DeLuise could go all day without getting a usable scene shot…
Also, my favorite part of a Jackie Chan movie is always the outtakes they run over the credits. Hysterical.