Articuno, Moltres and Zapdos - Ultra Ball(i hate them)
Mewtwo - Ultra ball(took me 80 Ultra Balls,LOL)
Suicune(using Wobbuffet's Shadow Tag)-Ultra Ball
No Master Balls Used During The Whole Gameplay.
Never used it I always felt like using the masterball was just taking the easy way out and I thought it was fun trying to catch the legendaries, especially the Eon twins trying to trap them with pokemon like Golbat w/ Mean Look or Wobbuffet's Shadow tag.
Kyogre- Had 123 ultra balls. After I caught it I had 4 left. (Bought)
Groudon- Pokéball 4th try
Rayquaza- 36 Ultra Balls
Latias- 73 Pokéballs
Latios- Master ball
Jirachi- Never caught....
Deoxys- A soft reseting record resulting in 529 Pokéballs to catch this beast.
3 Birds- 35 Ultra Balls each
Mewtwo- Didn't attack it, used one Pokéball... Caught it first try