Sadly, I wasn't able to find as many for MLP-The Simpsons as I was for SpongeBob-MLP, mostly because despite The Simpsons having way more episodes than both shows combined:

MLP:FiM- 135 (127 segments)
SpongeBob- 204 (389 segments)
Combined- 338 (516 segments)
The Simpsons- 596

They generally share less in regards to tone and overall feel, outside of a little bit of similarity in terms of humour, but pretty much every animated series since 1991 has had that with The Simpsons. Not only that, but I only wanted to do the first couple seasons (Season 1-9 plus the movie), not because the later ones are bad, but because the older ones are much more well-known and easier to get the references from.

1. The Tracey Ullman Show (the early shorts from the late 1980s were far less realisitc and appealling than when The Simpsons became it's own show, which some bronies can also say about most pre-G4 incarnations of MLP)
2. Bart the Genius (in a science experiement gone wrong near the end of the episode, Bart turns his skin green)
3. Bart the General (Nelson bullies Bart by shoving him in a trash can after school and having it roll back to his house)
4. The Call of The Simpsons (let's just say Homer and Bart weren't experts at living in the wilderness XD)
5. Life on the Fast Lane (Marge recieves a bowling ball from Homer for her birthday, which sucks because she has no skill in bowling)
6. Bart Gets An 'F' (at fear of having to repeat 4th grade if he fails his English test, Bart dreams of him (and his son) still being in the 4th grade many years into the future, which is unfortunately the truth now that the show's been running for 29 years)
7. Simpson and Delilah (Homer doesn't get a wig per se, but uses a hair growth formula that instantly makes everyone love him)
8. Dancin' Homer (Homer becomes the mascot for the Springfield Isotopes baseball team, which his gig being having to put on a silly dance at every game)
9. Bart Vs Thanksgiving (Bart has a dream of coming home, only to be scolded and laughed at by his entire family)
10. Bart the Daredevil (Bart's daredevil stunts get the attention of a ton of kids, leading to him forming his own fandom)
11. The Way We Was (flashback episode to when Homer and Marge were in high school in the 1970s, no not the 1990s, are you mad?)
12. The War of The Simpsons (seriously, this scene has always reminded me of Homer's ridiculously drunk memory of the previous night's party from said episode)
13. Saturdays of Thunder (Homer and Bart build a go-kart to race)
14. Homer's Triple Bypass (Homer is hospitalised)
15. Marge Vs The Monorail (this one should be pretty obvious, both episodes have song numbers that borrow the same reference)
16. So It's Come To This: A Simpsons Clip Show (April F-)
17. Homer's Barbershop Quartet (Homer tells the story of how he joined a barbershop quartet similar to The Beatles, 22 years before Pinkie Pie did the same thing with the actual Beatles 100X faster)
18. Rosebud (Mr Burns reunites with his childhood stuffed animal, a teddy bear name Bobo)
19. Boy Scouts 'n-the Hood (the Simpsons and the Flanders men get stuck on a raft in the middle of the ocean after a boy scouts trip gone wrong)
20. The Simpsons Halloween Special/Treehouse of Horror V: Time and Punishment (Homer time travels, causing a butterfly effect that constantly makes the future worse)
21. Round Springfield (Bleeding Gums Murphey's ghost appears to Lisa in the form of the head in a cloud)
22. Who Shot Mr Burns? (Mr Burns blocks out the Sun from Springfield in order to power his electric heat lamps)
23. Team Homer (more bowling!)
24. Scenes from the Class Struggle in Springfield (Marge starts hanging out with snooty, high-class people and alienating herself from her own family, honestly these episodes are eerilly similar)
25. Hurricane Neddy (after a string of bad luck, Ned Flanders has a nervous breakdown and yells at everyone in Springfield)
26. The Mysterious Voyage of Homer (sunrise, sunset, sunrise, sunset, ad infinity)
27. In Marge We Trust (get it?)
28. Homer's Enemy (Frank Grimes loathes Homer because he isn't as stuck up and intelligent as himself)
29. The Secret War of Lisa Simpson (TTTTTEEEEESSSSSTTTTTIIIIINNNNNGGGGG.)
30. The Joy of Sect (The Simpson family joins a cult that's essentially as far of a portrayal to the Church of Scientology as they can get away with without Nancy Cartwright (who's part of that religion) quitting like Issac Hayes with South Park)
31. The Simpsons Movie (one of the most well-known aspects of the movie is Homer's adopted pet pig, Harry Plopper)
32. Couch Gags (for those of you who haven't watched the show, let alone the title sequence, these are essentially running gags near the end of the opening where The Simpsons run into their living room to watch TV and something cartoony or just outright random happens, either along the way or once they sit down, here are some examples )

Got any I may have missed, or even some from Season 10 to the present? Let me know in the comments below.