Mulder has carried (in order I believe) a Sig 226, a Glock (probably 19), a S&W 5906, a Sig 228, and a Walther PPK as a backup.
Scully started with a Sig 230, then Glock, then 5905, then 228 (her current weapon). She's also used a PPK on occasion.
The show only matched the Bureau when the agents carried Sigs. Scully and Mulder carried Glocks when the FBI didn't authorize them, and now that the Bureau issues Glocks, Scully and Mulder are back to Sigs.
By the way, the second "Deep Throat" carried a Sig 229 .40. There's a great line of dialogue when he explains what it is and what it will do as he threatens to kill Mulder.