This has been done a thousand times over, but in any case, my favorite Legendary is Entei. Though he's not very good in the games, with such a limited move pool, I love his appearance. He looks bold, powerful, fast, elegant, and get-in-my-way-or-I'll-run-you-over all at the same time.
Diaruga is another favorite of mine. Again, I like his appearance and color scheme. Being able to control time is awesome.
Aruseus is neat as well. I find that he has a lot of potential to have a great, deep background story, and the "thousand arms" bit from its Pokédex entry can be interpreted in a lot of different ways. I don't see Aruseus as being the God of Pokémon though, or at least not in a literal sense. I see him as being somewhat like the Ellimist from the Animorphs book series - revered and maybe even worshipped, but still just a living, breathing being. A manipulator, an all-powerful weakling, if that makes any sense.