My favorite is by FAR Pokémon Vega, a masterpiece of a hack. Sure, it's Japanese, but it's SO professional that, whether you understand it or not, it's a must to play. It takes place in a whole new, arctic region, made from scratch with completely new tiles. There is a physical/special split and beside the Fakémon, there are also fake moves. A LOT of new moves, even, a lot of which I'm surprised Nintendo haven't come up with yet. There is a large number of Fakémon related to existent Pokémon; these evolutions usually have fantastic designs and are seriously powerful, much like a lot of other Fakémon. The overall Fakémon designs are flat-out fantastic and incredibly creative, with some of the best fake Starters and Legendaries ever, in my opinion. The music in this hack, though. It's such a delight to hear Pokémon Vega's music, as it's so varied from Route to Route, from battle to battle... I mean, from a hyperintense Gym Leader theme to perhaps the most sinister music possible for a Pokémon villain.
All in all, Pokémon Vega has given me a VERY good outlook on ROM hacking and has shown me how incredibly talented fangames can be. I recommend this gem of a hack to everyone on this forum. Go play this game and spread the word of it.
On a side note: Pokémon Vega has two predecessors, two Emerald hacks named Altair and Sirius. The successor hacks to Vega, Pokémon Procyon and Deneb, are in development.