My favourite Gen 3 Pokemon is Salamence. It's strong, fast, has a diverse movepool, a great hidden ability, and I love its design.
Other favourites of mine are Sceptile, Blaziken, Swampert, Ludicolo, Swellow, Gardevoir, Breloom, Ninjask, Shedinja, Hariyama, Sableye, Flygon, Milotic, Cradily, Dusclops, Gorebyss, Metagross, Regice, Latios, Rayquaza, Jirachi, and Deoxys.
Honorable mentions: Linoone, Beautifly, Dustox, Shiftry, Pelipper, Masquerain, Mawile, Aggron, Medicham, Manectric, Wailord, Camerupt, Torkoal, Grumpig, Cacturne, Altaria, Seviper, Solrock, Crawdaunt, Claydol, Armaldo, Regirock, Registeel, Kyogre, and Groudon.