By far my longest save ever was on Pokemon Y with over 600 hours on it. The reason for this was me starting to get into competitive battling more after Gen 6 came out so I spent too much time breeding for perfect IV Pokemon, EV training them, building strong teams and then battling online. I was also shiny hunting a lot back then so at least around 150 hours were spent shiny hunting with different methods (Masuda method, chain fishing, friend safari and horde hunting).
The second place goes to my White 2 save with around 350 hours on it. This save is pretty much a 100% completed White 2 game because I did everything you can do in this game. I beat White Treehollow, Pokestar Studios, every tournament in PWT, beat the E4 with a Monotype team with almost every type, leveled up every shop in Join Avenue to their max level and I also completed the living Unova Pokedex on that save. I also did some shiny hunting in double grass but only found one shiny, a shiny Camerupt after almost 14k random double grass encounters.