Children of the Gods is the movie-length pilot of Stargate SG-1. It is said that there were creative differences between the producers and the networked “Showtime” chipped in, too. Additionally due to the story-telling of the series some aspects don’t make sense anymore.
Thus someone decided to create a “Final Cut” version of the pilot where scenes are reordered, shortened and the FX were enhanced.
Changes that were made (in loose order):
The (in)famous full frontal nudity scene of Sha’re was re-cut. She’s still naked but one does not see it anymore. Back then Showtime insisted on the scene to push the MPAA rating up. But since SG-1 is supposedly a “family show” this was deemed inappropriate. This is one change I don’t mind. The scene never bothered me (why should it?) but it’s no loss either. But from where I am standing, I could start an argument on why a show where most people carry weapons of some form and were people get killed on a weekly basis (and we’re talking big bloody staff weapon wounds) somehow becomes “family friendly” just because they cut out the 20 seconds nudity scene.
In the original version, Apophis captured that female Air Force officer, brought her into his harem, then also captured Sha’re. Then he tested said officer, deemed her unworthy, killed her, tested Sha’re and implanted the Goa’uld. Now he captures the officer, kills her, captures Sha’re and implants the larva. No harem. In combination with the above nudity scene the pilot showed how Humans are merely “walking meat” in the eyes of the Goa’uld. They have no regard for the value of human lives. They are just slaves for them to command.
This ruthlessness gets lost in the new version. Here Apophis takes only what he deems necessary as if he would actually care. Don’t know why they did it but I don’t like it.
Earth has no DHD (keyboard to open the gate), they built a computer to do the work. But in the original version Apophis magically opened the gate without using the computer. Now one hears him shout a command and it sounds as if his Jaffa are dialling out manually. That’s OK.
Another FX change is in regard to the Death Glider. The pilot had a never seen again version of the Death Glider that has a ring transporter system. They added an additional Tel’tak (a transport vessel later introduced in the series) and made it look like as if the Tel’tak activated the ring transport. That’s OK, too.
They also removed the scene where Kawalsky is taken over by a Goa’uld (which is addressed in the episode after the pilot). That makes somewhat sense for a stand-alone movie but even then they could have let it in.
They also removed the scene where Kawalsky doesn’t know that O’Neill had a son. That makes sense, because it’s later established that they’ve known each other for many years.
But what I really didn’t like were some changes in the pacing and in Sam’s introduction. In the original version there’s some bantering between the old gang and Sam when General Hammond introduces her (topics: She’s a woman and a scientist). That and when it comes up again when they meet Daniel was all cut out. But instead they used alternate cuts of the scenes or simply cut it out. Now the flow is gone. Some of the scenes end with a long pause before the next camera angle. It’s like the actors are waiting for the director to shout “cut”. It happens all the time, especially in the beginning. There’s no natural flow anymore.
I always liked the joke about the location of Carter’s reproduction organs, especially because they make fun about it later in the series.
And they removed the MacGyver joke! 
So my final judgement is that I can’t think of anyone who actually needs this “Final Cut”. 