One of those funny ideas was that the Gremlins gain control over the movie for a short time. In the theatrical release, it looks like a broken reel, followed by Gremlins messing around and inserting an own movie. Luckily, Wrestling superstar Hulk Hogan (at the peak of his career at the time) is sitting in the audience and convinces the Gremlins to continue with the actual movie.
Some of the audience at the time report that often especially the younger people were looking for either Gremlins or the Hulkster in the auditorium.
Nevertheless it was clear that this joke would lose much impact on tape or on TV. So it was decided to insert an alternative scene for the VHS version which would have a similar effect on the home audience that had often been annoyed by messed up tapes. In this version, it looks like the tape is messed up and the Gremlins have taped over it. They switch through several channels and it ends up in a John Wayne movie where the Duke 'convinces' the Gremlins to return to their own movie immediately.
On the DVD-release, you again have the theatrical version with Hulk Hogan, but the alternative scene of the VHS version is included as easter egg.
However, some fans who didn't know the theatrical version did complain about the missing John-Wayne-gag (which already had happened vice versa at the release of the VHS-version)...