Pokemon Mega Adventure is a hack which takes the main theme as Mega Evolution. Since the day it was invented, Mega Evolution is one of the most useful methods to evolve and make your Pokemon stronger.
Pokemon Archaic Legacy is a Pokemon fan-made game by using RPG Make XP. There is a region called Akiria which contains a lot of secrets of this world. Well, it has appeared from nowhere in ancient times.
Pokemon Uranium: Usually, a project which has been developed for a long time is worth waiting. And so does Pokemon Uranium, a fan-made 9-years Pokemon project.
Pokemon Obsidian is a great Pokemon Hack with nice graphics and good storyline. This game is made by Justin, who owns two other Pokemon Hacks before and Pokemon Obsidian is the third game of him.