The 2 that come to mind are Brazil: Criterion Collection and the upcoming Dawn of the Dead: Ultimate Edition. I believe each of these has 3 versions of the movie (Theatrical version, director's cut, etc.). Was curious to know if there were any others available...

T2: UE

Alien Quad. has 4 different movies with alternate cuts.

Kate & Leopold and The Abyss each have two cuts.

-Almost Famous
-Recent Disney titles

The Leopard, the DVD includes the full length Italian language version, and also includes the shorter U.S. version with English language. Criterion probably wanted to be able to present Burt Lancaster's voice on the English version (he's dubbed into Italian on that version) but since the lengths of the two versions aren't the same they presumably couldn't just include two language tracks as not everything on the longer version was dubbed into English. Also the Italian is presented at about 2.2:1 aspect ratio, as if prepared for a 70mm presentation; the U. S. version is 2.35:1 from a 35mm print.

My Darling Clementine
The Gold Rush

Legend with Tom Cruise. Has the original theatrical release with Tangerine Dream's score, and Ridley Scott's director's cut with a totally different orchestral score by Jerry Goldsmith.

Brazil only has two cuts (though it has three discs). But it's still an amazing set.

Butterfly Effect
Independence Day

The American cut of 'Brazil', with one line not found *anywhere* on the Criterion disc, is still not available in any way. Apparently, the bare-bones disc is actually the proper director's cut found on the Criterion disc, it's just mislabelled.

X-Men (and 1.5) has two cuts available via "seemless" branching.

the old Manhunter limited edition had two cuts, one which was not-quite the theatrical and one which was not-quite the director's cut.

the old Halloween limited edition had the theatrical and the TV versions.

Strangers on a Train, both the old disc and the upcoming new one, British cut and American cut (though the new discs lists "American cut" and "preview cut", I think)

I believe 'Crash' had the R-rated and unrated.

Highlander: Endgame has an R-rated version on one disc and the theatrical "earlier" cut on the other disc.

All four movies in the Alien Quadrilogy
Die Hard
Identity
E.T.
Monty Python's The Meaning of Life

Criterion's "Indiscretion of an American Wife/Terminal Station." From Criterion's Web site:

De Sica’s version, Terminal Station, was screened at a length of one-and-a-half hours, but after disappointing previews, Selznick severely re-edited it and changed the title to Indiscretion of an American Wife without De Sica’s permission. The Criterion Collection is proud to present both versions of this controversial release.

Supergirl had a limited edition with two cuts

Criterion's "Scenes From a Marriage" had both the US theatrical and the original miniseries length, I think.

Several 'Mystery Science Theater' discs have both the original "uncut" movie and the episode-versions of the movie (in addition to the characters talking, there are also major cuts to the movies).

Bad(der) Santa

Identity (I think has an alternate ending)

Stargate UE

Not exactly. The disc has an icon that will pop up to take you to deleted footage in non-anamorphic letterbox. This is far from seamless, and this does not actually constitute a new "cut" of the film.

American Wedding Unrated has both the unrated and rated version of the film.

Criterion has 3 versions of The Killers: Siodmak's 1946 version, Siegel's 1964 version and Tarkovsky's 1956 student film version

Curse of the Demon

yes you are correct

The Abyss has the theatrical cut and the director's cut that actually causes the ending to make sense.

James Cameron's Titanic docu: Ghosts of the Abyss contains the theatrical IMAX cut and an expanded 90min cut of the film.

I put seamless in quotes *because* it's not quite seamless, but I did think that you could pick an option which showed all the scenes edited in, it was just an awkward jump into and out of the new scenes.

But it's been a while since I watched it, so you're probably right.

No, the question was for single releases with multiple cuts, not multiple cuts over multiple releases.

Two of the myriad of 'Army of Darkness' releases had both the theatrical and the (improperly restored) director's cut ... the two-disc limited edition and the "Boomstick" edition. [Correct me if I'm wrong on that latter; I forget which it is, aside from it has two discs, because I have the R3.]