For fat burning, there's a number of different ways that are great.
I'd recommend staying away from things like stair master or incline treadmill, because if you're doing cardio, your ONLY goal should be to increase your heart rate, NOT put strain on your muscles.
Personally, I use the elliptical machine for about an hour 6 days a week. Elliptical is excellent because it doesn't damage your joints the way treadmill or jogging would. However, elliptical doesn't burn calories as fast as other methods of cardio.
The BEST form of cardio is jump rope when it comes to burning calories as quickly as possible.
Regardless of whatever kind of cardio you do, always make sure you're doing some sort of interval. This means, say, you're doing elliptical, I'll go as hard as I can for 60 seconds, then go easy for 60 seconds. I'll do this for my whole workout. The trick is to make your heart beat fast, then slow, then fast again, then slow again, and so on and so forth. This should apply to ANY cardio you do.
For muscle, it depend on your goal. If you want to get big muscles, lift heavy weights for 3 sets of 6-12 reps. To get cut, lift lighter weights for 3-4 sets of 15-25 reps. Regardless of which one you're doing, try to pick a weight that makes the last 3 reps difficult.
There's plenty of excellent exercises out there for muscle building so I'm not going to list them. The key thing to keep in mind is to make sure you're doing compound exercises. This means the exercises you're doing should work multiple muscle groups rather than isolate a single muscle. For example, push ups and pull ups are excellent because they require to use a variety of different muscles.
One last thing, don't ever work out the same muscle groups without letting them rest for a day. For instance if you work out your biceps one day, work out something else the next day.