My list of the best of the best.
Starship Exeter "The Tressaurian Intersection." Scripted by BBS denizen Dennis Bailey, you can blame this project for drawing me into posting on Star Trek message boards at all. Watching it as it was released was, for me, a life-changing experience.
Star Trek: New Voyages "To Serve All My Days," scripted by D.C. Fontana. I'm probably in the minority, but I like this one much better than "World Enough and Time." The twist ending is shocking and truly inspired.
Both episodes of Star Trek: Aurora by Tim Vining. These are outstanding.
The TAS-style shorts for "The Best of Both Worlds" and "Threshold" by Gazelle Automations.
Yorktown: A Time to Heal. This is an unusual project of historical significance, successfully completed with impressive results.
This isn't to say that I don't think other efforts aren't also good. For example, I've enjoyed many episodes of Farragut, Intrepid, and Potemkin. The level of drama in the teaser of Star Trek: Intrepid "Heavy Lies the Crown" is especially worth mention, as it packs a dramatic punch that is more powerful than the teasers of most canon episodes. Star Trek Continues had amazing production values, but I never thought its stories were on the same level as that of their other strengths. YMMV.
No doubt I've overlooked something, so suffice it to say, this list is incomplete.