In Emerald, I wanted to get on with the story so I threw the Master Ball. I did it for Crystal (Suicune) too, and I'll probably through it at Giratina in Platinum. I just hate catching legendaries. Too much of a bother, in my opinion.
I used an Ultra Ball. I taught my Groudon dragonclaw which is super effective against dragon types so did alot of damage and usually put it into red hp. This mostly forced it to use rest so when i attacked it again it was in red hp aswell as having a sleep status problem which makes it ALOT easier to catch. Still didnt work first time though :/ persistence is pretty vital for catching yourself a rayquaza without a masterball. The battle could go on for sometime so pack yourself some timer balls too
I used my masterball on Latios.