Gary Emerald is one of the foremost experts on Star Trek props and costumes and has even written for Star Trek: The Magazine on the subject. He recently posted some interesting insight into the history of Star Trek props and costumes on the big Movie Prop Forum message board. Here is what he has to say:
"There was a ton of Star Trek stuff released to a certain collector in the mid 90s, and I mean so much stuff it was offensive, mainly from ST: TNG. This collector had KEY ST: TNG stuff, he was connected with high ups at Paramount. A lot of what showed up in the Profiles in History auctions over the years from ST: TNG were from his collection including the Khan.
There were items that were stolen over the years and were placed on a list that Paramount was looking for, and if these items showed up at a high profile auction, convention or anywhere they would have been pulled, so the Khan that was sold was not one of these costumes that Paramount was looking for. This individual had the Trek stuff openly displayed and had this stuff not supposed to been released it would have been confiscated. There was no secret where it was and who owned it.
My friend bought the Khan, I built the display for it. There were two other Khans at the studio, one clean and the other distressed. I am assuming these were cherry picked by the top brass, at some point cause Christie's did not offer Khan at their sale. If Paramount still had it, Christies are idiots for not offering it.
I have heard many individuals who were involved with the series did get to select a few mementos from Trek , and of coarse I would assume they did not pick back-ground first and second season jumpsuits.
I know that most Trek fans on this board seem to like ST: TNG and beyond. I focus on the 60s series, and literally almost every 60s costume has been accounted for. One collector I know, involved with Trek's production has at least 4 60s Kirk tunics. I can also state that most of the key props from the Trek feature films TMP, ST WOK, ST III, ST IV have been in collections for years. Also key working ST: TNG props are long gone as well.
Wonder why Picard's chair was not offered at the Christies sale over the summer? It was sitting in the hot sun in a parking lot as recently as July of 2006, thrashed. Not everything gets saved either."
I hope that offers some insight on the history of where some of the stuff is. Gary is always a great source of info on the subject and is well respected in prop collecting circles.