My Top 5 are in 2013...
1. Ruby Destiny: Life of Guardians. It has a very deep story which connects everything in the Ruby Destiny Universe and a nice gameplay, which is supposed to be difficult. Now I'm etching to Broken Timeline.
2. Sovereign of the Skies. The only good German hack I know with a very good story which makes this game a bit untypical, especially Team Tundra and Deoxys. And I like the small Golden Sun references.
3. Vega. It's a japanese hack with very good quality and maybe one of the few fangames where I have enjoyed with Fakemon. I can't understand the text, but the story and music are really amazing.
4. DarkViolet. At first I was skeptical, but the "revamped" Kanto gives me a reason to try. And I loved it, especially the changes like a second rival, more Team Rocket encounters and a actual story, which make this hack more a Red/Green remake than FireRed/LeafGreen (sorry, no offenses, but I like DarkViolet more).
5. Liquid Crystal. Now this is what I called a "Crystal Remake". I like the new features and added story. I still hope it will be completed, so I can travel the Orange Islands...