In my opinion, It was Pokemon Ruby Destiny: Life of Guardians too.
The storyline to all Destiny series is connected and the events as well.
It's very challenging and you need to be smart enough to pull it off.
My favourite is Pokemon Jupiter Version, not because I made it, but because it's so ****ed up that I honestly can't believe I made it before learning of the magic that is "marijuana". Looking back, it helped me get into programming, but it's so retarded, that I can't help but look back and piss myself in laughter thinking about it.
Since neither the title nor 1st post specifies it has to be a Pokémon hack, I'll actually take a different route here. Perhaps the GBA hack I admire the most is Bregalad's Sound Restoration hack for Final Fantasy VI Advance. The work put into that to make the game's music both tolerable and masterful again really fixes the release's one major flaw.
If we're strictly talking about Pokémon, though, I'll throw my hat in for Flora Sky. Amazing hack in so many ways.
1. Liquid Crystal
Beautiful remake of crystal and physical special split make this my fave hack
2. Pokemon Glazed
Great hack overall.. Beautiful tiles and great story.. But it hasn't finished yet and the ending was a little anti climatic..
3. Pokemon Resolute
Not the most beautiful hack, but the biggest one.. I hope the hack will be finished soon..
4. Pokemon Flora Sky
The most completed hack that even features emerald's battle frontier!! Too bad this hack doesn't have physical special split.. If it has, flora sky will be my number 1..
5. Pokemon RD: Life of Guardians
A great hack overall, and I love the story
Pokemon Glazed,Pokemon Resolute, Pokemon Flora Sky, Pokemon Ruby Destiny Series
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. Souvereign 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. 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...
5. Flora Sky. This one is a very good hack on it's own right with many features like the C-Apps and the nice graphics. But the story bugs me from times to times, because it sounds more like a mash of the Shaymin plot of the Giratina movie and the story of Pokémon Emerald...
I don't think I can really rank mine. :s My favourites are all so different.
Firstly, Pokemon Shiny Gold holds a special place in my heart. The phrase "I joined for Shiny Gold" couldn't be any more apt for me, and it was the first ROM hack I ever played and helped get me into ROM hacking myself. It was the first G/S/C remake and introduced a host of new and old features. A really good hack, it's just a shame it never got finished.
Funnily enough, Shiny Gold's rival hack Pokemon Brown/Prism are both good hacks too. How different they are and how much content they have is just amazing. Every once in a while I'll go back and play through Brown again. It feels so fresh too since the legendaries change with every playthrough. Prism is set to be an amazing hack too and I wish Coolboyman the best with his hack and future endeavours.
Another hack I like a lot, for similar reasons to SG, is Crystal Dust. I really loved Crystal (it's one of my favourite Pokemon games and I have a lot of nostalgia for it :p) and I love how much it tries to stay true to the original. It's the best remake of G/S/C imo.
Other hacks that deserve props are Quartz/Marble (despite the "controversial" Pokemon I loved these games so much! :D), Sienna (again, it's a shame it was never finished ) and Light Platinum (again, a really fun hack and the graphics are exceptional! :D)