I did a search for Star Trek scripts and found this Index of folder at http://leethomson.myzen.co.uk/, that is just chock full of modern and retro TV scripts in an easy to browse directory. In addition to classic shows like Star Trek and Quantum Leap they also have modern shows like Dexter and Smallville. As a bonus they have a much smaller folder of TV show bibles. If you are interested in TV writing or want to look up your favorite show, it is a great source.
If you are a big Star Wars fan you might want to check out the venerable The Jedi Bendu Script Site, Starkiller. It is a site dedicated to looking critically at the original drafts and concept art associated with the movies that would become Star Wars. According to the site they have three goals (which I think they pursue quite admirably)
* To pursue and find (photocopies of) early drafts and screenplays of the original trilogy (A New Hope, The Empire Strikes Back, Return of the Jedi) and the prequel trilogy (The Phantom Menace, Attack of the Clones, Revenge of the Sith).
* To pursue and find (photocopies of) storyboards from the aforementioned films, by such artists as Alex Tavoularis, Ivor Beddoes, Irvin Kershner, Joe Johnston et al.
* To pursue and find (copies of) rare photographs or film clips detailing cut scenes or angles not normally shown in the films themselves.
* To pursue and find (copies of) blueprints, floor plans, call sheets etc. from the films.
If you are a fan who wants an education on the films, this is a no-brainer. There is literally days of content for you to dig through. I have been going there for a while and I still find myself lost some nights for hours in what “could have been”.