While there can be no definitive "best" team in Pokémon, there are tier lists that rank the best Pokémon in each generation based on their stats, effectiveness in battle and ranking against other Pokémon. Due to new moves, new Pokémon and new type match ups in every generation, these tiers change in every game. For Pokémon Emerald, the best Pokémon are those in the third generation uber tier.
There are nine official tiers in Pokémon: not fully evolved, little cup, never used, borderline 3, rarely used, borderline 2, underused, borderline, overused and uber. The uber tier contains the most powerful Pokémon. The third generation uber tier is comprised entirely of legendary Pokémon except for Wobbuffet and Wynaut. These include Mewtwo, Mew, Lugia, Ho-oh, Latias, Latios, Kyogre, Groudon, Rayquaza and all forms of Deoxys. However, it is worth noting that this only includes six of 17 available types in third generation Pokémon. Therefore, a team including only these Pokémon may not match up well against other teams solely due to type disadvantages. It may be worth using Pokémon from the more diverse overused tier. These include Pokémon such as Gengar, Rhydon, Umbreon and Raiku. It is also important to consider EV training and abilities. With proper training, even a Pokémon from one of the lower tiers can stand up to an uber or overused.