Had to think a lot about this..i loved every episode.
 

Okay, thinking over it.  
Most to least favorite:
 
The Crystal Empire  
Magic Duel  
Too Many Pinkies  
Apple Family Reunion  
Sleepless in Ponyville  
One Bad Apple  
Wonderbolt Academy  
Magical Mystery Cure  
Keep Calm and Flutter On  
Games Ponies Play  
Just for Sidekicks  
Spike at Your Service

Games ponies play is last.
 
I haven’t seen Spike at your service yet.
 
 
I’d probably put Magic Duel as the best.

So many great episodes, I had to think a lot
 
1: Sleepless in Ponyville  
2: The Crystal Empire 1 & 2  
3: Wonderbolts Academy  
4: One Bad Apple  
5: Spike at Your Service  
6: Games Ponies Play  
7: Magic Duel  
8: Just for Sidekicks  
9: Too Many Pinkie Pies  
10: Keep Calm and Flutter On  
11: Apple Family Reunion  
12: Magical Mystery Cure

Magic Duel  
Wonderbolt Academy  
Games Ponies Play  
The Crystal Empire  
Too Many Pinkies  
Sleepless in Ponyville  
Apple Family Reunion  
Spike at Your Service  
Keep Calm and Flutter On  
Just for Sidekicks  
Magical Mystery Cure  
One Bad Apple

1- Keep Calm and Flutter On  
2- Just for Sidekicks
 
I haven’t decided on the rest.

@Background Pony  
Iron Giant kind of pissed me off because of that. So much of the movie was just boring and meh and just generally sucked, and then that ending kidney-punched me right in the feels. ;^;

Iron Giant’s pretty alright. About what you would expect would happen if a giant alien robot crash-landed in mid-Red-Scare America. Nothing will prepare you for the eventual feels, though.  
Nothing.

@Battle GT  
Could’ve been Spike At Your Service.

Sleepless in Ponyattle  
Just For Awesome Sidekicks  
Apple Family Reunion of Laidback-ness and Quaintness  
One Bad Johnny Apple Seed  
Too Many Gosh Darn Pinkie Pies  
Keep Calm and Flutter On Until the Awkward Ending  
Magical Not So Mystery Cure  
The Crystal Empire Strikes Back (Pt. 1 & 2)  
Spike At Your Mixed Bag of Service  
Boringbolt Academy  
Boring Games Boring Ponies Boring Play  
Magic Diarrhea Duel of Pus Infested Boils

@Battle GT  
People are making their own ranking lists in the comments.

I don’t rank ep’s of shows, to much wiggle room. Now favorite movies, that I can do.

Just for Sidekicks nowhere near the top 5
 
This list sucks

Iron Giant is pretty amazing for the feels and for Dean.
 
Dean is AWESOME.