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