MMA, which stands for mixed martial arts, is a relatively new sport that is just starting to get real athletic talent. The problem with the sport early on was that few athletes grew up learning martial arts or training how to compete in MMA, so the really athletic people were at a severe disadvantage when fighting against highly skilled fighters. They may have had better conditioning workouts, but the other guys knew how to execute chokes and knew how to strike much more effectively. Now that everyone knows what MMA is all about, conditioning workouts have become much more important than they once were.
The reason for this is that the skill gap is starting to close - people know most of the disciplines involved in MMA, so they are at least able to defend and execute attacks to significant effect. So what's the best workout to get great conditioning for MMA? Well, you'll have to realize that it varies from person to person, but you'll want to focus on high intensity cardio and you'll want to increase your anabolic conditioning. The best way to do this is to use primarily power exercises when training.
Some examples of power exercises that are useful for MMA are: overhead squat, power cleans, snatches, push-pulls, and a whole slew of plyometrics, including depth push ups, box jumps, depth jumps, and lateral jumps. All of these will push your conditioning to its limits. You can combine some of these exercises with other ones to even further condition yourself - consider a clean and press. That's a great exercise that'll put a ton of strain on your body.
Few more workouts that you might want to consider: upright row, bent over row, shoulder press, deadlift, squat, and shrugs. These are not power exercises per say, but they will build great strength and power in multiple muscles throughout your body. Remember the key is to make your workout as versatile as possible. The more you shock your body, the better your workout will be. Since most of an MMA fight is done in an anaerobic state, we'll focus on heavy lifts to do that.