I remember that even back when I first got Sapphire, I didn't use the Master Ball on Kyogre. Actually, I went and used in on Rayquaza instead. It's a Level 70 already, so I might as well have. And then I did the same in Emerald. When I replay those two though, I save it for Lati@s.
In Platinum, I only used the Master Ball for Mesprit, because my god there were too many roamers.
In Black and White, my Master Ball was reserved for Tornadus. In Black 2/White 2, I don't think I even used it at all xD Actually, in those games I seemed to have the most luck [catching two of the Swords of Justice at full health with Ultra Balls].
And finally, now in X and Y I haven't even touched them. Granted, I'm at the E4 anyways, but I don't really plan to use it. At this point they're more like trophies than anything. And even when I'm tempted to use em', I try to convince myself to save it for something better. Even when there usually isn't xD