It really repends on, well...a LOT of things, like what flops along WITH it - I like the idea of trips, because a boat beats a flush in the event BOTH are possible. AND trips will beat 2 pair if the str8 & flush posibilities don't cause a threat after the turn (rare but it happens) BUT, lets say the board flops the pair. Is the 3RD card in the flop a flush draw that YOU don't have? Is it a connector card to the set (that could give sometime a straight draw? What else is in your hand? Also a chance that if the 2 cards for the set are hole cards, are there overs on the board? If a higher pair hits the board, you could get beat by a bigger boat - happens more often than you'd think.
In a nutshell, I love being double suited, but a flush draw is still a draw. I MUST have something else going on, like straight draw or 2 pair. I prefer trips on the flop if it's a rainbow, and/or not connected, and might bet out quickly. Position is also important, as always - as well as how many are in the hand. Each card as it comes though.