In Generation 5, I did not use a single Master Ball. I do think that it is a little cheap to use it, but I can name one case where I think it is absolutely necessary: (Unless you want it to be challenging.) In XD: Gale of Darkness, not using the Master Ball on Shadow Lugia would make the following battle with Greevil very difficult, because Lugia would have heavily weakened your team.
3DS Friend Code: 4012-4489-0237
My Friend Safari: Ground with Sandshrew (Slot 1), Camerupt (Slot 2), and Diggersby (Slot 3).