The Last of the Mohicans (Michael Mann)- Is in an ultimate cut. The theatrical release is no longer available and OOP which has extra and alternative scenes.

Alexander (Oliver Stone) - Is in an ultimate cut. The Alexander Revisited version is no longer available which had extra footage. The theatrical cut also makes use of extra footage. Not that good a film though started watching it and pushed stop on the theatrical cut.

The New World (Terrence Mallick) - I believe is now only in it's extended cut of which I am yet to see but I have the theatrical version on DVD. The EXtended cut is now on Blu-ray without theatrical version I believe.

Although Highlander (Russell Mulachy) was not updated all the remaining footage of extra scenes were destroyed in a fire at where the Reels were stored. The Full Soundtrack to the film has never been Properly released only in a low quality bootleg. Destroyed footage

A duel sequence that introduced an Asian immortal named Yung Dol Kim was cut from the film. The footage for the scene, along with certain other deleted scenes, was later destroyed by fire, although a few stills from the sequence, some in colour and others in black and white, survived.
Connor, Kastagir and Bedsoe partying at a bar. The scene expanded more on Kastagir and Connor's relationship and revealed that they met during the American Revolutionary War.
One scene in which Connor shows Brenda his katana after the sex scene.

http://www.imdb.com/title/tt0091203/alternateversions

The Keep (Michael Mann) Film Disowned and butchered theatrical cut of original vision. The extra scenes are not lost though apparently but locked away in a Paramount Vault

47 Ronin (Carl Rinsch) - Film radically altered in post production, original film has never been released publically before studio intervention. And director compromised vision.

Barveheart (Mel Gibson) - original VHS cut scenes lost, DVD version in the UK was censored of throat slit scene of the new Mrs Wallace's captor. Now restored in Blu Ray version but many other violent scenes have been censored that have never been shown.

(Rambo) First Blood (Ted Kotcheff) - US TV version had many extra scenes and dialogue. Never been released as deleted scenes on any release Various Censored versions in other countries from international edit.

The Shining (Stanley Kubrick) The film was recalled whilst in theaters and the ending was removed to make a new ending by Stanley Kubrick's request then all the footage was destroyed except save one reel apparently the estate may be in possession of it.

Enter the Dragon (Robert Clouse) - Theatrical cut only available on Laser disc. All versions are the Uncut version which has music and sound missing. And a missing scene. No deleted footage for this film has ever been made available although some did to feature in other films after Bruce Lee's death.