I often try to check-raise all-in, or bet then reraise all-in with a pair and a flush draw. In your situation, I would definitely reraise all-in after your opponent raises the minimum. He's probably too weak to call an all-in reraise, and even if he does call, you're a favorite over most pairs, and have roughly the same chances of having the winning hand on the river against two pair, providing one of your cards is higher than the highest of your opponents two pair.

When I have a big draw like this, I like to force my opponents to gamble or forfeit the pot. I don't like to passively call raises or check-call, since my chances will diminish on the turn if I miss, and my opponent will likely slow down if I don't. Playing these situations passively also creates the problem of allowing a better flush draw to stay in the hand.