It’s hard picking just 3 but mine are probably:
- The Host - S02 E02
- Detour - S05 E04
- Agua Mala - S06 E13
But… these were close
- Orison - S07 E07
- Quagmire - S03 E22
Hmmmmm top three.
These always stood out for me. The entire show was total gold
Monday S06 E14 Lady is groundhog daying herself, Mulder, and Scully dying.
Dreamland 1 and 2. S06 E 4-5 Body switching with one of my favorite actor/comedians, Michael McKean
They are the same story, so the two episodes are really one long one with a cliffhanger in-between
And
Josè Chungs from Outer Space S3 E20
because of Alex Trebeck and Jessie Ventura as the Men in Black, and Lord Kinbote