Look for anomolies:
Stats that are too high or too low for level: Level Zekrom 100 with 3 Speed or Level 1 - Pikachu with 500 Speed. The highest HP you will see is 714. The highest stat you will see is 614. 999 is impossible.
Weird Pokeball: If you have a Pokemon in a Cherish Ball that has never had an Event, it is hacked.
Illegal Moves: Like Pikachu knowing Draco Meteor.
Illegal Abilities: Bulbasaur with Drizzle. This also applys to Pokemon with Hidden Abilities that have not been released yet (EX: Raikou).
Has not been released yet
Shiny Illegally: Victini, Zekrom, Reshiram, etc. are programmed not to be shiny, so if they are, they are hacked.