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It's Rayquaza. Definitely.
First game was Emerald (I was about 10), and even reaching it at the top of its tower was a challenge which took me awhile to complete, and when I got there I was pretty fucking pumped to capture Rayquaza. I caught it (in my Masterball I think), and it became the staple if my team, along with Blaziken (I was 10, give me a break). Of course, Rayquaza being a Level 70 son of a bitch, it completely demolished the E4.
I transferred it from Emerald, to Pearl, then to Platinum, then to SoulSilver, and there is where I think I lost it. Didn't transfer it to White, because fuck Gen V.
I don't use legendaries anymore, but when ORAS comes out, I'm gonna fucking catch the Rayquaza, name it what I named my old one, and give it a plebeian, high power moveset like I gave my old one just because I fucking can and will.