In 2006, CBS went back to the archives and created HD prints of every episode of the show. In addition to the new video transfer, they re-did all of the model shots and some matte paintings using CGI effects, and re-recorded the original theme song to clean it up. These "Enhanced" versions of the episodes aired on syndication and (as of the time of this writing) are planned to be released on DVD.
From mid-1998 to early 1999, the Sci-Fi Channel aired Star Trek in a 90 minute weeknight slot as a special edition, airing every episode produced in their original order, complete with footage that hadn't been seen since NBC originally aired the show. It also contained commentary on each episode by members of the cast and crew. The first run through the Special Edition was hosted by William Shatner. Leonard Nimoy took over as host for the second run, but the Special Edition was taken off the air in the middle of this run.
The episode "The City on the Edge of Forever" features background music on the VHS and laser release that's different than the broadcast version. The original music has been restored for the DVD release.
A one-hour retrospective on Star Trek featuring Leonard Nimoy was produced in 1983 prior to production of Star Trek III. This videotaped special is often syndicated and shown in Canada as the 80th episode of "Star Trek" (1966). An edited version of the original pilot, "The Cage," was sometimes syndicated with the series in the 1990s, just before the Sci-Fi Channel obtained exclusive rights.
Footage from the episodes "The Trouble with Tribbles" and "Mirror, Mirror" was used in a special episode of "Star Trek: Deep Space Nine" (1993) in the late 1990s entitled "Trials and Tribble-ations," which featured the stars of DS9 digitally inserted into the original footage.
In Germany some episodes were cut or rearranged during the dubbing process (for example in the episode "Amok Time" the dialogue was changed to Spock having a disease). The episode "Patterns of Force" has never been shown on TV due to the Nazi-thematic. It was only released in the late 90s on VHS.
The second pilot of the series, "Where No Man Has Gone Before" was originally cut a bit differently than the version that exists on VHS and DVD. In the original cut, there is an opening narration by Captain Kirk stating: "Enterprise Log: Captain James Kirk commanding. We are leaving that vast cloud of stars and planets which we call our galaxy. Behind us: Earth, Mars, Venus, even our sun are specks of dust. A question: what is out there in the black void beyond? Until now our mission has been that of space law regulation, contact with Earth colonies and investigation of alien life. But now, a new task; a probe out into where no man has gone before." followed by the words "STAR TREK" appearing on screen. They fade away and are replaced by "STARRING WILLIAM SHATNER." The episode then moves into act one, with the words "STAR TREK ACT I" appearing on screen. The episode then proceeds as normal until Scotty says "It's begun transmitting, sir." at which point, the words "TONIGHT'S EPISODE 'WHERE NO MAN HAS GONE BEFORE'" appear. After which, there is an extended pan of the Enterprise hallways with the titles "CO-STARRING LENOARD NIMOY AS MR. SPOCK" appearing and fading away, followed by "GUEST STARS GARY LOCKWOOD AND SALLY KELLERMAN." Over this scene, the red alert klaxon blares and Lieutenant Kelso repeatedly saying "Bridge to all decks. Condition: alert!" We also see Gary Mitchell walking around the corridors as well until finally cutting to Kirk and Spock entering the turbolift, at which point the episode continues as normal. Additionally, the end credits were much different in this original cut. Instead of the normal "Star Trek" theme playing, a different piece is used and the credits only credit the supporting characters; none of whom are referenced by name. (For example: PAUL FIX AS: SHIP'S DOCTOR, GEORGE TAKEI AS: CHIEF PHYSICIST, JAMES DOOHAN AS: ENGINEERING CHIEF, etc.)