Another interesting list here: http://tvtropes.org/pmwiki/pmwiki.php/KeepCirculatingTheTapes/Film
A very interesting list. Quite a few of the entries have been shown on British TV. I specifically remember watching Looking for Mr Goodbar at one point.
Some more contenders…
The extended (by 7 minutes) version of Colors has never been made available beyond the LD and VHS releases.
(Slightly) extended version of Blue Thunder: some of the P&S VHS/LD releases contain additional footage during the car chase sequence. All of the subsequent home video versions, including the Blu-Ray are taken from the theatrical release. This alternate version has turned up on TV in the past.
The expanded edition of Lawrence Kasdan’s Wyatt Earp was issued on NTSC LD and VHS but nothing else since.
Ridley Scott provided an audio commentary track for the LD of G.I. Jane but it has been omitted from the subsequent DVD and Blu-Ray.
The steamier version of The Carpetbaggers, which was renowned for its (at the time) fairly adult scenes is apparently unavailable on DVD, or even LD. It appears that Paramount have erroneously used a censored master.
Men Don’t Tell - Golden Globe nominated drama starring Peter Strauss, originally aired on CBS and based on the true story of a battered husband. It’s been shown on Lifetime and other channels but there has never been a home video release or (in the US) further over-the-air broadcasts, allegedly due to ire from a number of women’s groups towards the storyline.
Nicholas Meyer produced a widescreen, director’s cut of The Day After - featuring an audio commentary track. It was released on a special edition LD but hasn’t been repackaged for DVD/Blu-Ray.