* The main titles in the special edition start with an "Alien" organism, and when the camera pans back it is revealed to be a bug. The bug is then squashed by the thumb of a soldier. The shot continues to pan-back as the Auriga floats away from the camera.

* Ripley awakens from surgery (removing the Alien embryo), she grabs the surgeons arm and breaks it.
(15 seconds)

* Scientist: Let's try this one..... Ripley? Ripley? Ripley what is it? Ripley, Ripley...
(10 seconds)
Right after General Perez, Gediman, and Wren leave the mess-hall after showing Ripley8 pictures of a glove and fruit, the doctor shows Ripley a drawing of a young, blond girl, which appears to trigger an emotional response.
(5 seconds)

* After Ripley repeats Gediman's 'Fiori 16', he asks her what she remembers. This is when Dr. Wren can also tells some more about the Weyland-Yutani company ("bought up by Wall-Mart")
Gediman: Hard work. We used blood samples from Fiori 16 on ice. Where you died. We've remade you...we've cloned you.
Ripley: Fiori 16?
Gediman: Does that ring a bell? Are you remembering something?

Military: They [Weyland-Yutani] had defense contracts under the military. They went under decades ago...getting way before your time. Brought out by Wal-mart. Fortunes of war.
(about 28 seconds combined)

* Several smaller segments are added:
Elgyn: Want anything?
Hillard: Yah, how about a cup of coffee?
Elgyn: Anything else to wet yoru mouth?
Hillard: A little milk
(12 seconds)

* Elgyn: Vriess, Call, 'bout time we're gonna dock.
(3 seconds)

* Vriess: Hey Call.
Vriess: What has two thumbs, one eye, a pink tongue, and screws like a god?
Call: What
Vriess: Two thumbs a pink tongue, and screws like a god?
Call: What?
Vriess: [Motions that he's screwing]
(53 seconds)

* Vriess: It's about time we started associating with a better class of people.
(7 seconds)

* The Betty introduction scene has been completely re-edited, in addition to the extended dialouge sequences mentioned above. The scene now starts with the Betty flying towards the Auriga, Elgyn giving the clearance code over the radio (E-A-T-M-E), but now he flirts some more with Hillard, and warns Call and Vriess over the intercom to get ready. Next, Call and Vriess are shown working on the cargo, followed by some extended dialogue in which Vriess tells Call an obscene joke. This is followed by the scene in which Christie gets his hidden weapons (which came first in the original cut). Next is Johner's 'target practice', Vriess then throws a tool to his head, Call calls him names, but Johner simply replies by asking for his knife. When Vriess comments on his alcoholism, Johner demands his knife back, Call breaks it, Johner threatens her, and there is an extra line from Vriess that he and Call deserve better company.

* During the deal between Elgyn and Perez, Elgyn has some more 'flattering' remarks about Call:
Elgyn: Mighty handy with a monkey wrench too i might add. I think Vriess has a bit of a light in his eyes for her. Fine little ass like that can make a man walk, you know what i mean?
(16 seconds)

* After Elgyn asks Perez for three days bed and board, Perez agrees under a few conditions:
Elgyn: If it's not imposing
Perez: I don't see any problem. Couple of conditions.
Elgyn: Conditions?
Perez: Not you, nor any of your formindale crew members will go anywhere near restricted areas. Rule #2. No trouble. Good behaviour.
Elgyn: Good behaviour.
Perez: No fights.
Elgyn: No fights.
Perez: No fights.
Elgyn: No fights.
(35 seconds)

* After Purvis shouts "What's in-fucking-side me?!?":
Wren: "A parasite! A foreign element!"
(4 seconds)

* After Call says that Purvis can be frozen and operated later, she has another run-in with Johner, followed by Christie agreeing that Purvis comes, but saying he will shoot him if he starts acting funny:
Christie: Look, he comes with us. We freeze him on the Betty and a doctor can remove it later.
?: Fine with me.
Johner: Since when were you in goddamn charge?!
Christie: Since you were born without balls!
Vriess: Ease up people.
Christie: Alright you come with us. You might even live. Get twitchy on me and you'll be shot.
(30 seconds)

* Just before everyone takes a dive through the flooded kitchen, Christie and DiStephano have a short conversation on Christie's weapons ('the disposable kind'), and Call reminds everyone to take a deep breath.
Christie: You ready to get wet partner?
Vriess: Yeah!
Distephano: Hey ahh.. ..will your weapons fire underwater?
Christie: Yah they are disposables, they can take it.
Distephano: Disposables? hey, i heard about those, yah. How many rounds?
Christie: 20. ??? split points give you a good hold you can get a smaller caliber
Distephano: That's cool.
Christie: The're big with hitters cause you can throw them away after a job. no-one likes to throw away a weapon they are attached too. you know what i mean?
Distephano: Yeah.
(47 seconds)

* In the chapel, just after Purvis's false chestburst, there is an extended line from Call, stating she recalibrated ground level, sending the ship into an uninhabited quadrant of Earth, before she mentions time of impact. After Ripley asks if she's the new asshole model, she replies she couldn't let humanity annihilate itself. Ripley comments that she once tried to save people as well; she remembers a girl that had bad dreams, but she died despite her help, and now she can't even remember her name. After DiStephano enters to take them with him, Ripley asks Call if she dreams, which Call does thanks to neural processors; Ripley says she dreams about the aliens every night, and that she used to be afraid, but not anymore, since it is always worse when she wakes up.

* Call: Ground level recalibrated. New destination 760403. Uninhabited quadrant. Rating systems offline acceleration increase.
Call: I couldn't watch them do it. I couldn't let them annihilate themselves. Do you understand that?
Ripley: I did once. I tried to save...people. It didn't work out. There was this girl she had bad dreams, I tried to help her. She died. And I can't even remember her name.
Distephano: I guess we're almost there.
Ripley: Right. Do you dream?
Call: I...we have...have neural processers....Yes.
Ripley: When I sleep I dream about them..it. Every night. All around me. In me. I used to be afraid to dream, but not anymore, because no matter how bad the dreams get when I wake up it's always worse.
(1 minute, 17 seconds)

* After Johner kisses Vriess for getting them safely through Earth's atmosphere, there is an alternate ending with the Betty landing on Earth. Call warns Ripley for the military that will come looking for her soon. She says someone can get pretty lost on Earth, and asks Ripley what to do. Ripley replies that she doesn't know, since she is a stranger there herself. The camera then goes up, to reveal a what looks like a post-apocalyptical Paris.
Call: So this is Earth, huh?
Ripley: This is Earth.
Call: Ths is my first time here. I suppose the military will be sniffing around here pretty soon. I bet youre not to anxious to see them.
Ripley: Not Really.
Call: A person can get pretty lost around here if they wanted to. What do you think? What should we do?
Ripley: I don't know. I'm a stranger here myself.
(1 minute, 15 seconds)

* This was mentioned by Joss Whedon in an interview in Cinescape, and it's the scene from the script where Ripley is laughing her head off while the aliens are running amuck. He also stated that he wasn't sure if it was in the latest cut of the film at that time. [Thanks Doug Skiles]

* Another was mentioned in some pre-released test screening reviews, and was Ripley's mention of Newt, who she calls "a girl" that she tried to save, but couldn't. It went something like: "You remind me of someone. A girl I knew. I tried to save her, but I couldn't... I can't even remember her name..." I don't think that's exact, but moderately close. It was just a couple lines of dialogue right around the "why did you come here?" dialogue in the chapel scene. [Thanks to Doug]

* Apparently, there was a planned scene where an alien 'stimulates' Ripley. Whilst cocooning her, it runs its hands about her body with the 'secreted resin' and when it goes between her legs, it presses all the right buttons. Jeunet and Weaver wanted it. Fox didn't. [adapted from alt.cult-movies.alien newsgroup posting]

* There was a very clear shot cut and edited. It involved a chestburster also bursting through Wren's head. This edit was shown in the several 'making of' segments, both on "Entertainment Tonight" and other shows. The shot had Purvis, after being shot, do exactly what he did in the theatrical release, which was to go behind Wren. In the theatrical version, the chestburster also rips through Wren. in the cut shot, the burster is able to rip its way through Wren's skull and out his upper head with much more gusto.

* Cinefex Magazine issue #73 (Starship Troopers on the cover) there is a large article on Alien Resurrection. Near the end of the article they talk about how the Auriga was blown up.
The way it is described is nothing like what is shown in the film. The FX crew said they set up charges along the length of the ship and detonated them one after another creating a segmented explosion to simulate the ship breaking up upon atmoshperic reentry. This is never seen in the film, but the trailer for the video game shows a very similar shot fitting this description.
My guess is the ship was to explode upon entering the atmosphere in one version of the script, but when the ending changed they had to cut it. Instead they put in that weak fireball effect on the Earth. [Thanks Crescent!]

* While the ending to the film has several variations from the script, late reshoots in post production modified the ending (when Call and Ripley look down over earth.) This is possibly as a precursor to Alien 5.