The aspect ratio of Star Trek VI was altered to 1.85:1 on the 2004 SE DVD and the director also included the following visual alterations:

There is a new wide shot of Scotty reading the blueprints of the Enterprise in the dining hall.
Valeris’s interrogation scene has been entirely reedited. There are now close up shots of Kirk and McCoy when they speak their lines instead of being in wide shots. When Spock and Valeris name a particular conspirator, the face of that person briefly appears in a flashback like style.

The colour timing on Do The Right Thing was altered by the cinematographer for the 2009 anniversary edition.