Hoenn's Super-Ancients are really cool-looking and the biblical-ish mythology adds a special kind of epic. Their battle music is fittingly ancient and godly.
Altogether, the Regis are the creepiest Legendary trio, and I like how they fit into the mythology as well, being golems. The whole RSE sidequest (which is actually kind of a challenge) to unseal them makes them that much more mysterious. Regirock is my favorite of them.
Regigigas is cool-looking, but useless because of Slow Start. This is a sad thing.
I also like Entei, Deoxys, Palkia, Giratina, Arceus, and Zekrom.
☆ Bulbapedia has a walkthrough project! Spread the love! ☆
Palkia epic Water Dragon type. Only one weakness.
Mewtwo, who grew into a legend even though he shouldn't even exist. Most badass pokemon ever.
Zapdos, since I love thunders and he owned Pikachu.
Groudon, he can swim in lava, he is evil, and he can screw all water pokes, even though his weakness.
Dialga, it controls time and is very very strong. Who among us wouldn't want to control time, frankly now.
Articuno. Its cry is the best one out there.
Kyogre. Just Kyogre. Drizzle+ Thunder= Awesome.
Smart enough to use forth in the wrong context
Claims: Metagross and Travis Touchdown