Rarely. I try to catch everything in one type of ball (usually a normal Pokeball).
The only times I've used a Master Ball is when I'm trying to catch all the Pokemon, where I'll use it on one of the last Pokemon that's usually a hassle to catch (such as those that run away). If I'm just catching legendary's, I may use it on the last legendary I have to catch, though that's only if I'm feeling lazy at the time.
I didn't use one in X&Y.
The only times I've used a Master Ball is when I'm trying to catch all the Pokemon, where I'll use it on one of the last Pokemon that's usually a hassle to catch (such as those that run away). If I'm just catching legendary's, I may use it on the last legendary I have to catch, though that's only if I'm feeling lazy at the time.
I didn't use one in X&Y.