Red, Leaf, and Blue.
Lyra, Ethan, and Silver.
Brendan, May, and Wally.
Dawn, Pearl, and Lucas.
You can say Kris, Ethan, and Silver if you want, but I don't consider her to be a seprate character from Lyra so I didn't list her.
For me, it's a tie between the Gen 1, Gen 2, and Gen 4 trio. I don't think of the Hoenn trio as a trio. I prefer them individually with the protagonist, or as I think of it, May-Brendan and May-Wally.