Rayquaza (Ruby and Emerald version), Regirock, Registeel, Regice (think these three were in Emerald too. might be Ruby instead), Regigigas (Diamond), Azelf (Diamond and Platinum), Uxie (Diamond and Platinum), Mesprit (Diamond and Platinum, believe it or not ~.~), Giratina (Diamond), and Heatran (Diamond, possibly Platinum too). Anything not mentioned was either not seen or caught with a Master Ball.
Oh, and if you want to count them... Moltres, Zapdos, Articuno, Entei, Raikou, and Suicune several times on XD/Colosseum.
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I prefer not to use a master ball on legendaries. Even to the point of refusing to use it. In fact i got Platnium again so i can recatch Giratini and creselia without using a master ball
I don't really use my Master Ball on anything nowadays. Often it's just sitting there, collecting digital dust. I just, sorta refuse to use it. I generally want more challenge than that.
I believe I've caught Kyurem with some sort of ball, can't remember what it was but it definitely wasn't the Master Ball. I also caught Zekrom with an ordinary Timer Ball.
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Using a Master Ball is too precious, so definitely any Legendary Pokemon who don't run away from a battle. This even includes the Pokemon with a catch rate of 3! With many examples to list, I guess it's easier to list Pokemon I would have catch with a Master Ball if able (because with the chances of meeting one, it would be a better choice): Raikou, Suicune, Entei, Latias and Latios.
Thanks for reading.
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All of them :D
I never use masterballs.
As everyone may know, it's very hard to catch Legendary Pokemon with Pokeballs besides a Masterball. For all the Pokemon I'm about to list, I had to use probably over 20 Pokeballs to catch them. I started to stop using Master balls when I played the 5th Generation game, Pokemon Black & White. For most of the Legendary Pokemon, I used Timer Ball.
1. Suicune: Ultra Ball
2. Victini: Great Ball
3. Cobalion: Timer Ball
4. Virizion: Ultra Ball
5. Terrakion: Nest Ball
6. Kyurem: Timer Ball
7. Zekrom: Timer Ball
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I have never used a Master Ball and I never will. All legendary pokemon are easy to catch for me. It just takes skill and patience.
I have caught just about every Legendary Pokemon without a Master Ball, except for maybe Mewtwo in Pokemon Blue. However, the most memorable of these was my very first time I tried to catch one without a Master Ball. It was Rayquaza from Ruby... I wasted all of my Ultra Balls, All of my Great Balls (I had 99 of each kind), and it came down to my last 7 Poke Balls. I ended up catching Rayquaza with my third Poke Ball, and I currently have it in my White Version XD
Articuno (FireRed, Platinum)
Moltres (FireRed, Platinum)
Mewtwo (SoulSilver, with a Love Ball :D)
Lugia (SoulSilver, Net Ball)
Latios (SoulSilver, Fast Ball)
Mesprit (a pain in the ass, these three)
Zekrom (cheap catch with a Quick Ball)
Reshiram (same as Zekrom)
Kyurem (same as Zekrom and Reshiram)
Cobalion (another pain in the ass, recorded a 20min video of me flinging balls at the damn thing)
Ranma ½ fan. And I never got into shipping flamewars about it either.
I haven't used a Master Ball on a legendary since Platinum, where I used three of them to catch the bird trio. They were driving me insane. But I save Master Balls for the real emergencies. I'll detail a couple of hypothetical scenarios for you.
Scenario 1: Black Version. You've just gotten to the center of the Giant Chasm, and Kyurem's made it snow. On the way to the cave entrance, your last Super Repel comes out. You're out of any sort of Repel now. You enter the cave and run across it to get to Kyurem, only to be impeded by a wild encounter, just two or three squares away from Kyurem. You roll your eyes, ready to run away from the Boldore- OH SHIT IT'S SHINY! And you know that every single wild Boldore in the Kyurem part of the cave knows Explosion. Not having expected this situation, you have absolutely nothing with Damp. You were planning to incapacitate Kyurem with paralysis rather than sleep, and paralysis doesn't guarantee that Boldore won't attack. Thanks to Sturdy, you can easily wear it down, but there's no guarantee that it won't go boom on turn 1, and a Boldore at full health is not the easiest thing in the world to capture. Quick Balls are effective, but there's no guarantees. Then you remember, the Master Ball given to you by Professor Juniper. You had hoped to use it on Kyurem as a last resort, but Kyurem can be reset for. The Shiny Boldore, it's now or never.
Scenario 2: FireRed Version. You're in Cerulean Cave, on the maze floor. You've got the Max Repel a-going, and you have your Primeape smash one of the rocks. Wild encounter. As you grumble about how the Max Repel is supposed to prevent this kind of thing, you realize you're staring down the barrel of a Shiny Graveler. And you've heard all the horror stories. In the front of your party was your highest-leveled Pokémon- Charizard- to make sure the Max Repel did its job. You brought a Parasect with Spore to help with Mewtwo, but switching to Parasect will take up a valuable turn, more than enough time for Graveler to, as a certain Team Rocket grunt once said, "bye-bye a go-go". Even if Graveler doesn't explode during that switch, you check Bulbapedia and realize that Graveler's base Speed is slightly higher than that of Parasect's (you also learn that every single wild Graveler in existence, bar none, knows either Selfdestruct or Explosion), and both the Graveler and your Parasect are at level 55, so there's every possibility that Graveler will be able to attack (possibly by blowing itself up) a second time before Parasect would get a Spore off. Forget just chucking a Poké Ball at it. Graveler share a catch rate with Boldore, and it's not a favorable one. And as many, many, many disgruntled trainers will attest to, there's no guarantees where Shiny Graveler are concerned. And then you remember it; the Master Ball, sitting there in your bag, intended as a last resort against Mewtwo. But you fail to catch Mewtwo, big deal, so you reset. The Shiny Graveler, it's now or never.
Now that I come to think of it, I never really used a master ball on most legendaries - except Mewtwo. All the other legendaries weren't much of a challenge, and the runaways were actually fun to follow. But for some reason my game slowed down in HGSS dungeons and it took me over three hours to get to Mewtwo WITH Max Repels WHILE riding a bike and WITH a guidebook.... I got frustrated that I chucked the Master Ball at it.
All you need is M-E-G-A-N-E