Apparently I've...never posted in this thread?! How is that possible? Well, whatever, I'm posting in it now!
So, anyway my favorite episode is Magical Mystery Cure, and I'm 99.9% sure it always will be. I've seen it so many times, and every time it makes me emotional. Probably has something to do with the fact that Twilight is my favorite fictional character ever and that I love her whole arc, huh? And I actually think it not being a two-parter works in it's favor; less was more in that case, IMO.
Some other favorites by season:
1: Winter Wrap Up, Green Isn't Your Color
2: Read It And Weep, Hurricane Fluttershy, Lesson Zero, A Canterlot Wedding (Yeah, I know this one's cool to hate these days, but darn it, I still think it's a blast to watch)
3: Keep Calm and Flutter On
4: Princess Twilight Sparkle, Maud Pie, Testing, Testing, 1, 2, 3
5: Crusader Of The Lost Mark, Amending Fences, Rarity Investigates, Make New Friends But Keep Discord
6: No Second Prances, The Saddle Row Review, Top Bolt, To Where And Back Again
7: Celestial Advice, All Bottled Up, Rock Solid Friendship, A Royal Problem, The Perfect Pear, Fame and Misfortune, Once Upon A Zeppelin, Uncommon Bond, Shadow Play (I like season 7.)
I'm not a critical type at all; I just go by how episodes make me feel. Being a critical type was how I stopped liking MLP in the first place; it took the joy of it out of me. So I'd rather not do that again. This post was way longer than I planned, whoops.