If you're fairly sure that your opponent has outdrawn you, isn't it pretty clear that you should check?

I usually check, but sometimes will make a standard bet both for information and for value.

Check-raising seems like the worst option, since you risk giving a free card and are putting yourself into a position to commit a lot of money to the pot with a second best hand. If your opponent calls on the flop as though on a draw, then bets when the third flush card comes, in general, isn't he/she likelier to have a flush than not?