I noticed a certain gray mare keeps showing up in this list.
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Links

Ponies Creed: Sisterhoof by DarkBrony181: http://www.youtube.com/watch?v=-vQCXt9_YAg

Celestia's Banana Song by Holmani154: http://www.youtube.com/watch?v=nBINO0i5td0

Ultimate Showdown of Ultimate Harmony by SparrowFae: http://www.youtube.com/watch?v=GgLiA2Jch5Y

Friendship is Witchcraft 9 - Seed No Evil by SherClopPones: http://www.youtube.com/channel/UCJI4dS-3rg-VrlN8kfSMQnw/videos (Video is not currently available directly through the SherclopPone's account)

Project Thundercloud by Playerdotexe: http://www.youtube.com/watch?v=FWuwq8HTLQo

Fall of the Empire - Trailer by SillyFillyStudios: http://www.youtube.com/watch?v=Me9rxgjLWfM

Vinyl and Octavia - Sunrise Surprise by DILeak Studios: http://www.youtube.com/watch?v=AHyw2rqNop0

Smile HD by MisterDavie: http://www.youtube.com/watch?v=PqVVtaWd8Pw

I Am Octavia [Animation] by TehJadeh: http://www.youtube.com/watch?v=zZvGGGHekU4

Button's Adventures - Pilot Episode: http://www.youtube.com/watch?v=S2VhC1QF7ww

Honorable Mentions

Twilight's Day Off by OmegaOzone: http://www.youtube.com/watch?v=JPvTId6D6IU

PMV - Summer Sun Celebration by ChiefDoggingFood: http://www.youtube.com/watch?v=PFNtwSUX3ls

Paint The Town Safety Yellow by CaptainHoers: http://www.youtube.com/watch?v=GaVmKezs_4w

Opening Videos
The Fresh Prince of Mutton by MaydeEdits: http://www.youtube.com/watch?v=jv21lTvmyy0

Unstoppable PMV by EpicDarkWizard12: http://www.youtube.com/watch?v=Ya6aNZ0lesA

Credits song

Dash! by Waterflame: http://www.newgrounds.com/audio/listen/542003