pokemon adventures: Red's Chapter.
follows the same story as the manga and is super amazing! creative bonus chapters keep you going and the small but still massively impactive changes keep it interesting! a must play for anyone who has read the manga
I love Ruby Destiny series, personally. My favorite of them all, though, would definitely have to be Rescue Rangers. I was very fond of how they've incorporated all those Mystery Dungeon features into Pokémon Ruby; it was very creative. If they've made another hack like this at some point in the future, I would play it in a heartbeat. :] Second favorite is Reign of Legends, with Life of Guardians being third. Aside from Ruby Destiny, I'm also quite a big fan of Pokémon Light Platinum and Liquid Crystal.