It varies. For LeafGreen it has to be Mewtwo - I buy into the pokéSpe explanation that it was designed for Mewtwo, even if you do receive it from Silph Co. (I think). In HeartGold I think it was probably used on Mewtwo again - same reason, plus I like the appearance of all the special apricorn balls (now really concerned that as it's been to Sinnoh and I've deleted my HG file that my Latias won't be in a Fast Ball). In Emerald it's for Rayquaza - tradition, first time I got that far I used the Master Ball when it was about to KO my last pokémon.
On Diamond and Platinum it gets more varied. On Diamond originally I used it on Dialga, same for Giratina on Platinum. However, on my current playthrough I used it on Mesprit. And on Platinum I'll probably use it on Cresselia, as unlike Latios, Latias and the legendary beasts I don't like them enough to go chasing around the region for hours.