This is a discussion on Second Set on the flop in deep stacks within the online poker forums, in the Tournament Poker section; Will my game be correct if I make a call All-in with the second or third set on the flop if my stack is greater
It depends on the stage of the game and your place regarding the bubble. But generally flopping a set is a winner in my mind, and it may be useful to not always assume that your opponent is playing the current nuts.
If there are no straight or flush draws and the only hand ahead of you would be a higher set, there's not much you can do. Of course, preflop action could help you narrow their range down a little. No one would fault you for calling a shove there. You might also want to check ICM implications.
I think you did the right thing, I would do the same in your place. A set is a very strong combination if of course you are talking about hold'em. In Omaha everything is completely different, and there the second or third set is not the best combination. In hold'em with a set on your hands, you can safely go to all inn, unless of course there is no clear straight or flush on the flop, or a full house.
If you are over 100BB deep and you bet the flop there is raising and re raising and then the all in you have to realize there is a chance it is set over set. With 2nd set its 55/45 you are beat. There are times you will have someone going nuts with aces and 2 pair. I wont deny this but I go broke every time here. its sick when it happens but dont worry about it.