Delia97 (of MIBHQ.com) has another episode list composed by Kevin W.

   
My RPG links:
Forgotten Realms Chronicle
Ghostbusters Universal

If you have seen some episodes not listed here and are willing to send me a very short synopsis, I'll add it here and give you credit.

1. The Long So-Long Syndrome [aka The Long Goodbye Syndrome]
   Jay, the new agent, kills a Skralnian and is hunted by all Skralnians until Kay shows them his mucus.
2. The Buzzard Syndrome
   Kay takes on an alien hunter called the Buzzard while Jay plays with the intended catch - a cute fuzzy man-eating monster.
3. The Irritable Bow-Wow Syndrome
4. The Alpha Syndrome
   Rogue agent Alpha steals a Sentillian's second heart. Kay goes after him alone.
5. The Undercover Syndrome
   The Tarkan Trade Minister arrives for a conference. Jay goes undercover as his Tarkan bodyguard.
6. The Neuralizer Syndrome
7. The Symbiote Syndrome
   Alpha kidnaps Troy the Symbiote and becomes indestructible until Mama Symbiote gets involved.
8. The Inanimate Syndrome [aka The Farewell My Lovely Syndrome]
9. The Psychic Link Syndrome
   An Alsidian has been stealing human essences in response to having his picture taken. Kay uses a mental link to track down the alien.
10. The Head Trip Syndrome
11. The Elle of My Dreams Syndrome [aka The Big Sleep Syndrome]
12. The I Married an Alien Syndrome
    Jay and Kay go to Hollywood to investigate the disappearance of some alien actors.
13. The Take No Prisoners Syndrome

  

14. The Little Big Man Syndrome
    Fmecks kidnap a Worm they mistake for "the professor" to get his growth formula. It ends with a rumble between gigantic Fmelvin and a gigantic Worm.
15. The Quick Clone Syndrome
    Jay is tired and gets Elle to make him some quick clones. Alpha makes an evil Jay clone which steals Zed's brain. Jay's quick clones save the day.
16. The Heads You Lose Syndrome
17. The Dog Eat Dog Syndrome
    Drekk, a hot-handed alien, escapes on Earth. Frank the Pug helps MiB catch him, so Drekk wants revenge.
18. The Big Bad Bug Syndrome
19. The Jack O'Lantern Syndrome
20. The Sonic Boom Syndrome
    Aleen, Kay's old partner, stops on Earth while transporting Auduzi. Auduzi escapes using its sonic weapon. Jay and Edie track it down.
21. The Bad Seed Syndrome
22. The Fmall, Fmall World Syndrome
    Fmecks steal Arquillian body suits to break into a radar station. They try to amplify a death ray from Fmoo to Arquillia. Jay gets shrunk and the death ray destroys Fmoo instead.
23. The Black Christmas Syndrome
24. The Supermen in Black Syndrome
    Three aliens steal the Tomasitron Matter Amplifier and become superheroes. Jay, Kay, and Elle get a dose and it's superhero versus superhero.
25. The Star System Syndrome
26. The Blackguard Syndrome

  

27. The Worm-Guy Guy Syndrome
    Califatic bounty hunters take the Twins. Jay and a Worm get crossed in a teleport stream.
28. The Cold Sweat Syndrome
29. The Puppy Love Syndrome
    Weapons smugglers use Veronica to sweet talk Frank the Pug into revealing MiB secrets.
30. The Lost Continent Syndrome
    Quintoon tries to raise Atlantis - the aquatic alien tourist site - with the help of traitorous agent C.
31. The Way Out West Syndrome
    A metaphyte hatches in a cave in Arizona and heads for Phoenyx. Jay and Kay go back in time to the Old West to stop it.
32. The Mine, Mine, Mine Syndrome
    A queen Bug and the Emperor Worm both hide out at a swank hotel. The queen lays eggs, and the MiB freeze them all.
33. The Bye-Bye Worm Syndrome
    Who overloaded the MiB reactor and framed the Worms? Zelgar the janitor then tries to create a black hole on Earth.
34. The Lights Out Syndrome [aka The Permanent Midnight Syndrome]
    An alien shadow race goes to the Moon to put out the Sun and leave the Earth in darkness.
35. The Out To Pasture Syndrome
    Zed retires. Alpha brainprobes Jay to find out the location. Then Jay learns it is all a plot to catch Alpha.
36. The Sardines & Ice Cream Syndrome
    Fmecks steal the Brooklyn Bridge and other New York landmarks. Jay accidentally swallows a Bobolot's egg and gets pregnant.
37. The I Want My Mummy Syndrome
    A mummy escapes from a museum. It turns out to be a Hyperion scout trapped in stasis. He opens a gateway for a Hyperion horde.
38. The Baby Kay Syndrome
    Kay reverse ages into a baby as the Men in Black track down an ambassador's daughter.
39. The Bad Doggie Syndrome
40. The "J" is for James Syndrome
    Jay wrecks the LTD and gets terminated. Reinstated, he helps Kay stop a Queen Bug invasion.

  

41. The Musical Chairs Syndrome
42. The Spectacle Syndrome [aka The Spartacus Syndrome]
    The Worms - mistaken for Wurp Gladiators - get transported to Imperia, a Roman arena.
43. The Back to School Syndrome
    Jay goes undercover in high school to protect the son of a high-ranking alien. The Worms get involved in a kidnapping attempt on the football field.
44. The Opening Gambit Syndrome
    Alpha knows the secret of oil-sucking aliens from the past. Jay plays chess for information and Alpha escapes.
45. The Future's So Bright Syndrome
    A Worm timejumper from the future starts a Worm population explosion that takes over Earth. Jay ends up in the future helping human resistance fighters.
46. The Loose Ball Foul Syndrome
    Fmecks steal a microplanet which is slowly heating up unless it is returned to orbit. Unfortunately it's the size and color of a baseball.
47. The Hots for Jay Syndrome
    Jay eats Huntak salsa and turns into a human flame.
48. The Circus Parade Syndrome
49. The Virtual Crossfire Syndrome
50. The Breaking News Syndrome [aka The Bad Boys, Bad Boys Syndrome]
    An alien news crew follows Kay while Drekk returns for revenge. Ends in a rooftop showdown caught on film.
51. The Zero to Superhero Syndrome
    Illegal alien slash superhero Cosmosis is in town. Jay becomes Swiss-Army Man to flush him out. Meanwhile a real villain shows up.
52. The Endgame Syndrome (part 1)
53. The Endgame Syndrome (part 2)