Sapphire- Latias. I got the game around 8 months after it came out and found out that everyone hated the dang roaming pokemon ;p I also defeated Kyogre because I ran into the fight with only great balls...
Emerald- I still haven't used a master ball in any of my plays. I like to keep it to prove that I don't need to use it. As for other legendaries:
Kyogre- Don't remember how many but I do remember that I almost cleared my whole ball pocket out :-/ Checked back and emerald says I caught it with a timer ball.
Groudon- I actually remember getting mad because I used 99 ultra balls (I cloned them) and didn't caught it but captured it with a regular pokeball.
Rayquaza- Don't remember how many pokeballs but my game says I caught it with a luxury ball (I also cloned them)
Regis- I caught them all with great balls :D
Latios- Ultra ball