If the pitcher is a true Ace, you're going to start them every time out. The Greinkes, Lincecums, Halladays, Lees, Hernandezes, etc. of the world. After that you've got to look at a few things. The first of which is the quality of the opponent the pitcher is facing. If the opposing team's offense is powerful (Yankees, Red Sox, Rangers, Tigers, Angels, Rays types), you may want to consider sitting them, while you're going to want to start your pitchers against weaker offenses, especially in larger ball parks (the Padres at Petco, Dodgers at Dodger Stadium, possibly the Marlins at their new home park). Finally, as the week goes on, you want to pay attention to the pitching categories in your H2H match up. If you've got a nice lead in K and W, you may want to sit a guy to prevent the possibility of damaging your ERA and WHIP, because you stand less to gain in the counting categories.
One other thing I tend to do is check a sportsbook to see what Vegas thinks of particular match ups. If my pitcher is a heavy favorite, and the Total Run line is on the low side, I tend to have a better feeling about tossing a certain pitcher.