Got a Masterball. Finished the story. Found Rayquaza. Bam. Another added to the 'Dex.
I think most people caught Rayquaza with their Masterball, if they didn't use it on Kyogre/ Groudon beforehand. Face it, most people don't want to go up to a Lv 70 Dragon legendary with a few measy Poke/ Great/ Ultraballs (especially if they are SRing) - They'd rather go full throttle with the Masterball and get rid of any chance of screwing up and doing it all over again.
A bad thing on my part. I go exploring with level 30's and one level 45 just to train the others and next thing i knew my level 30 Swellow was faced against the Rayquaza.. So to save my swellow i used a masterball...
i actually got my rayquaza by using a ultra ball, got his hp to red with my lvl 69 blaziken, then on the fourth ultra ball i got it, i still have my masterball, got every ledgendary pokemon in hoenn including jirachi (got two real ones from the colloseum bonus disk i have) except latias, latios and deoxys. SHOULD I USE IT ON LATIOS?
I panicked the first time because my Swampert's ice beam almost KO'd Rayquaza, and he was the only pokemon I had that could stand up to Ray.
Still, from that battle onwards, I have loved TIMER BALLS. They're so useful for legendary fights like that one.