Most football gamers cannot count on two hands the amount of times they've had issues trying to stop a player who likes to use the quarterback as a glorfied runningback. In fact, the Michael Vick craze brought a whole new definition to the title “cheese-ball." Luckily, this year stopping the mobile QB is not an impossible task, and with a bit of pre-snap scheming you can make plays on the QB depending on how your opponent is playing.
The first thing you should do is figure out your opponent's tendencies. Usually players that roll out have very predictable play-calling patterns and roll-out decisions. Players either prefer the wide side of the field or just a certain direction. This is not always the case, but usually players that don't sit in the pocket aren't able to make plays by breaking the defense down pre-snap.
The second thing you should do is get a defense where you can sit back with 7 guys in zone. Usually Cover 2 plays work best for this...you can also do Cover 2 Man plays as well, but the general rule of thumb is to make sure you have a lot of guys defending the pass.
You can also hot route both of your defensive ends into contain type assignments to get them to rush outwards at the onset of the play to try to force the QB back inwards or rush him into a pass he doesn't want to make in coverage. If you know your opponent's roll out tendencies, pick the defensive end on that side of the field and use him manually. Using blitzes isn't a bad idea either if you have him figured out.
When the play is on-going be sure to always stay outside of the QB and try to force him inside. If he gets outside of your DE, there will be no one else to stop him from running. Forcing him inside to your other 3 defensive lineman gives you a distinct advantage. The goal here is to apply pressure and get a sack from time to time, but most of all, force turnovers and incompletions on bad passes.
Another way to counteract a mobile QB is to just drop 'em all into coverage, save a man or two, and dare him to try to run the ball across the line of scrimmage into your wall of defenders. When it's third and long and fourth and long (because let's face it, you'll be in this situation as a defender if you are playing a guy of this type), that forces him to throw the ball into a blanket of coverage that'll be awfully hard to pick apart.
It's all about the numbers game and without containing one part of a players offense you will have a tough time beating him on the other half. The game this year is more conducive than ever when it comes to keeping mobile QBs at bay, so hopefully with these tips, you'll be giving Mr. Cheesehead a bit of a headache in no time!