I would have to say my favorite set in the Pokémon TCG modified format is Legends Awakened. When Kingdra was released I feel it changed the game by placing a bigger emphasis on speed than there was before. I also am a huge fan of all the pixies that came out in the set; Azelf, Mesprit, and Uxie. You can find at least one of those Pokémon in nearly every single deck out there. Cynthia’s Feelings is a gnarly trainer too; getting an 8 card hand after one of your Pokémon is Knocked Out is great and a necessity for some decks.
(This post is a response to this poll. Be sure to take part in the discussion and cast your vote if you have not already!)