In no particular order...
The Post-Modern Prometheus. Possibly the most bizarre episode of series television ever created that doesn't have the name "Twin Peaks" on it. Freaks, animal-human hybrids, Jerry Springer, Cher...just genius.
The Unusual Suspects. Flashback to Mulder's first meeting with the Lone Gunmen. Cool, hilarious and so much fun that I can even forget that the lovely Gillian Anderson isn't in this one.
Can't remember the name of this one, but it's the first time we meet Donnie Pfaster the death-fetishist/serial killer and he kidnaps Scully. Just a great, creepy episode.
Again, can't remember the name of this one. I'll just call it the Genie episode. Hilarious. Mulder gets three wishes, wishes for world peace and gets it...because all the people disappear.
All of the Mythology stuff from Season 2 up to about Season 5 (it got way too convoluted after that). It's hard to single out a single episode, but Paper Clip and The Blessing Way are standouts.
Hard to pick just five. So many great shows.
EDIT
I didn't realize we were doing ten, now. That's what I get for not reading the whole thing before I post. Here's five more:
Triangle
Jose Chung's From Outer Space
Clyde Bruckman's Final Repose
Small Potatoes
Bad Blood
"What? Did your life pass before your eyes? Cuppa tea, cuppa tea, almost got shagged, cuppa tea..."