So, there's more soundfiles on the isms page, but here are some others not related to specific memorable quotes:
 

1. X-Files Theme
2. Gillian laughing ;)
3. Gillian and David (and possibly others) laughing *g*
4. Mulder's answering machine.
5. Scully's answering machine.
6. Gillian: "I was - I was a bad girl."
7. Gillian: "I was... strange."
8. Gillian: "It was good for me!" (this was said on the David Letterman show, ironically enough. *G*)
9. Scully: "Mulder....."
   Mulder: "What?"
   Scully: "Suck my dick" (blooper)
10. Scully: "This is a simple lie detector. I'll ask you a few yes-or-no questions and you just answer truthfully. Do you understand?"
    Homer: "Yes." [machine explodes] (the Simpsons Files)
11. "Agents Mulder and Scully... FBI." - Mulder, The Simpsons Files
12. Scully: "This is the worst assignment we've ever had."
    Mulder: "Worse than the time we were attacked by the flesh-eating virus?"
    Grandpa Simpson: "Ow! He bit me with my own teeth!"
    Scully: "No, this is much more irritating." (The Simpsons Files)