Season 1 (Before the black oil, the Cigarette Smoking Man, and the threat of global alien colonization, there were just "Spooky" Mulder and the sceptical Dana Scully investigating in some outstanding Monster-of-the-week episodes. Pyrokinetics, killer insects, ghosts and genetic mutants really dominate this season, only Deep Throat and some UFO crashes contribute to the conspiracy factor. Favorite episodes: Pilot, Squeeze, Ice, Eve, Fire, and Darkness Falls)
Season 2 (A number of mythology episodes hint at a global conspiracy involving alien abductions, genetic engineering and the ever-lurking Cigarette Smoking Man. Mulder's family history and of course Scully’s abduction are important aspects of this season. The cast is extended by suspicious agent Krycek and informant X. Favorite episodes : The Host, Duane Barry / Ascension, Aubrey, Die Hand Die Verletzt, Død Kalm, Humbug, Our Town)
Season 3 (This season, often being described as the strongest of all, expands its mythology by introducing the black oil, Scully’s implant and the shape-shifting Jeremiah Smith. However, numerous hillarious stand-alone episodes not only explore interesting paranormal possibilities but develop the show’s trademark humor, thanks to writer and director Darin Morgan. Favorite episodes : Clyde Bruckman's Final Repose, War of the Coprophages, Syzygy, Pusher, Jose Chung's From Outer Space, Quagmire)
Season 4 (The mythology gets even more complex when the Consortium is discovered, the shadow government including the Cigarette Smoking Man. While Mulder is infected with the black oil and Scully discovers she has cancer, a deeper, romantically ambiguous relationship develops between them. Monster-of-the-week episodes include invisibility, shape-shifting, golems and human inbreeding. Favorite episodes : Home, Unruhe, Tunguska, Never Again, Memento Mori, Small Potatoes, Elegy)
Season 5 (Something for everyone can be found in this rather short season: For the mythology buffs, the season’s bookends tease with new revelations about the vast government conspiracies, featuring the Lone Gunmen, Agent Krycek, and Mulder’s father and sister. Shippers can watch Mimi Rogers and Luke Wilson incite jealousy between the leads, while monster-of-the-week fans might enjoy a few, at some points hillarious, stand-alone episodes. Favorite episodes : Redux, The Post-Modern Prometheus, Kitsunegari, Chinga, Bad Blood, All Souls)
Season 6 (Following "Fight the Future”, the season struggles fitting the film into the TV chronology and picking up plot points left dangling from the fifth-season finale. The mythology, dominated by abductee experiments, the Syndicate’s plans and theories on the descent of human life, gives room to some funny episodes, ranging from time travel and demonic babies to body switching and a version of Groundhog Day. Favorite episodes : Dreamland I+II, Triangle, The Rain King, How the Ghosts Stole Christmas, Arcadia, Monday)
Season 7 (With the original conspiracy plot arc having fallen into a muddle of loose ends and the initial wish list of monsters-of-the-week long exhausted, it’s surprising to find some really good and innovative episodes here, where stories are told from a monster’s point of view or in a realistic “Cops” style. Again, romantic feelings become obvious between Scully and Mulder, who is featured as a lead actor for the last time. Favorite episodes : Hungry, The Goldberg Variation, The Amazing Maleeni, X-Cops, Hollywood A.D., Je Souhaite)
Season 8 (Enter Agent John Doggett! Declined by many Mulder fans, he quickly makes Scully switch roles to being the believer during her pregnancy and the hunt for the abducted Mulder. In addition to new Special Agent Monica Reyes, some old friends and foes including Skinner, Krycek, and the Lone Gunmen join the season again. Standalone episodes cover a man going backward in time, deaths aboard an oil rig, a contagion in the Boston subway tunnels, and creatures resembling bats and slugs.)
Season 9 (The last X-Files season started with high expectations for "going out with a bang", which of course led to some disappointments among the fans. During the season and the grand finale some longtime issues come to a head, while other new issues and plots arise. Doggett seeks out the missing Mulder and Scully tries to protect her gifted son with the help of the Lone Gunmen. With the replacements Doggett and Reyes warming up and generally being accepted, many say the show could have easily continued if the writing had been better.)
season 6 or 8
Season 3 without a doubt with 7 of my top 10 favorite episodes: The Blessing Way/Paper Clip, Clyde Bruckman's Final Repose, War of the Coprophages, Syzygy, Jose Chung's From Outer Space, and Quagmire. I tend to lean more toward the humorous episodes. :-) I believe I stopped watching after season 7.
I love the funny episodes too, and Jose Chung's From Outer Space is a classic!