Top 40 Episodes and Bottom 20 Episodes · 2:03am Feb 13th, 2016
A'ight, so this is top third and bottom sixth of MLP episodes. I decided to skew this list more to the top because there are a lot more good episodes than bad ones out there.
Also I'd put the pilot episode, Friendship is Magic, at #41/#42. Fairly solid introduction to the series. So these top 40 are those which are better than the pilot.
So without further ado - and yes, I'm including movies too.
Top 40 - these episodes made it largely due to their heartfelt moments, intelligent storytelling, and humorous moments.
40.) It's About Time
39.) Rainbow Rocks
38.) The Best Night Ever
36/37.) The Cutie Map
35.) Party Pooped
34.) Pinkie Pride
33.) MMMystery on the Friendship Express
32.) Castle Sweet Castle
31.) Hearthbreakers
30.) Testing Testing 1, 2, 3
29.) Rarity Takes Manehattan
28.) Tanks for the Memories
27.) Maud Pie
26.) Hurricane Fluttershy
25.) Filli Vanilli
23/24.) The Return of Harmony
21/22.) The Cutie Remark
20.) Lesson Zero
19.) For Whom the Sweetie Belle Toils
17/18.) A Canterlot Wedding
15/16.) The Crystal Empire
14.) Magical Mystery Cure
12/13.) Princess Twilight Sparkle
11.) Scare Master
10.) Slice of Life
9.) The Mane Attraction
7/8.) Twilight's Kingdom
6.) Luna Eclipsed
5.) The Last Roundup
4.) The Cutie Mark Chronicles
3.) Sleepless in Ponyville
2.) Crusaders of the Lost Mark
1.) Amending Fences
Bottom 20 - These episodes are where they are due to out-of- character moments, shoehorned plots, weak storytelling or being kind of boring.
20.) Princess Spike
19.) Games Ponies Play
18.) Family Appreciation Day
17.) Hearts and Hooves Day
16) Fall Weather Friends
15.) Inspiration Manifestation
14.) Feeling Pinkie Keen
13.) Baby Cakes
12.) The Show Stoppers
11.) Dragon Quest
10.) Boast Busters
9.) Over a Barrel
8.) Owl's Well that Ends Well
7.) Just for Sidekicks
6.) The Super Speedy Squeezy Cider 6000
5.) Putting Your Hoof Down
4.) A Bird in the Hoof
3.) Look Before You Sleep
2.) Spike at Your Service
1.) The Mysterious Mare-Do-Well
The fourth and fifth season tended to fare a lot better overall. The writers who weren't as good of a fit for the show left and some writers improved substantially. More of my favorites are in later seasons, I think the show was still looking for its niche at first and tried some things which really didn't pan out.