Rayquaza is the coolest in my opinion...
However, if you raise a Slaking to Lv. 100 and focus on it's stats, it is stronger than any legendary Pokemon.
Scyther, if raised properly as well, is as strong as a legendary Pokemon.
(Uncanny, isn't it? XD)
In terms of the strongest, it's Groudon. He may his counters, but after setting up he owns all. So there.
In terms of personal preference, Zapdos and Latias. Latias is one of few defensive-minded Pokemon that can dish a hit and Zapdos has unique typing and has been my favourite of the Legends.
Hm.... this is tough, but my favorites are Articuno, Mewtwo, Suicune and Lugia. But my favorite out of all of my favorites is most likely Lugia... it's so cool! ;249;
me? well since i own all legendaries (cept for legit mew and deoxys which dont obey since they hacked) my uuber team of legendaries(dont ask i was bored) mewtwo is da best