Will fill this out further as I work on it- these were the first few that came to mind pretty quickly- you will note that the episodes of X-files are early ones- all considered classic by fans.
SN Episode X-Files Episode Common Theme
1-2 Wendigo 1-5 The Jersey Devil Wild Man/Creature suspected of cannabilism
1-2 Wendigo 1-19 Shapes Indian skinwalker legend Wendigo undertones on X-files
WENDIGO has a triple play actually as Charmed 1-12 The Wendigo is the one where Piper is turned into a Wendigo—- this is refered to I don’t know how many times in the next 2 seasons whenever they come across some shapeshifting demon/ spell to turn someone into something else. “Remember when Piper was turned into the Wendigo?”
1-6 Skin 1-14 Genderbender 1st time in each show we see a shapeshifter, Genderbender also has 1st appearance of Nicholas Lea who comes back later as the duplicitous Agent Alex Krycek, in Skin it is first time Dean is really charged with a major crime to his own name
1-6 Skin 1-19 Shapes Skinwalkers in both
1 – 8 Bugs 3 – 12 War of the Coprophages Insects terrorize small town
1-8 Bugs 1-20 Darkness Falls Insects terrorize folks in the woods in X-files- nature reclaiming the forest ( THANK YOU theblackgoddess in the CWLOUNGE!)
1-10 Asylum 1-8 Ice Unknown forces causes people to turn on each other violently, rampant paranoia ensues
1-15 The Benders 4-2 Home Nothing paranormal- icky redneck, backwoods incestuous Deliverance action in both
1-17 Hell House 3-20 Jose Chung’s From Outer Space Goofy joke episodes that have all kinds of inside jokes and are funny
1-17 Hell House 6-15 Arcadia Both episodes are funny- X-files has Mulder and Scully playing house in the perfect southern California subdivision- both episodes feature people being terrorized by the same Tibetan thought form
1-20 Dead Man’s Blood 5-12 Bad Blood Vampires living amongst us! X-files guest stars Luke Wilson, very comic episode, Supernatural has Daddy Winchester joining his sons on a hunt – Dean thinks the concept of Vampires is just hysterical
2-2 Everybody Loves a Clown 2-20 Humbug Strange things happen amongst circus folk
2-4 Children Shouldn’t Play With Dead THings 4-15 Kaddish Both have people bringing back loved ones from the dead with dire consequences…..
2-11 Playthings 5-10 Chinga Little girls play with creepy dolls and people die– X-files written by Stephen King set in a quaint New England town, Supernatural episode set in Connecticut inn in quaint New England town, episode feels like a Stephen King novel in a traditional creepy haunted manse.