Some of the old single player games had buttons on both left and right. For a two player, the standard would be buttons on right. But hey, if it's your machine do what you like. Home field advantage. Everyone will always ask why your buttons are on the wrong side though.
If you are talking about whether the player one is on the right or left period.... I'd say left nearly always. But again, if it's your machine do what you want. Be prepared for the confusion though.