Exercises to condition and muscle up a horse?

  So I am working with a 9 year old 16.3hh QH/Mustang. He has been stalled and not ridden or exercised in 4 years. He was recently turned out to pasture during the summer, in which he has lost weight since he can run freely . But even now he's a little chubby, but not bad. I lunge him often for a beginning exercise. But I want to know good exercises under saddle that will condition him and muscle him up. Any ideas? Thanks!
Try some ground work with him. Put him on a lunge line, and trot/canter him. You'll be forming a bond with him, and exercising him at the same time. Also, just try riding him, and take him for a nice lope . My horses absolutely loves loping after being in his paddock for so long. I've seen this one girl, and she rode her horse bareback, and had this large crop, and she had no reins, but just gently touched the horse's neck with the crop, and she actually taught the horse how to do turns and gaits without reins! It's really amazing!
Along with some of the other answers that are pretty good, try long trots. Just gradually increase the distance and let him get into a 'swing' and just trot out a few miles with walks and maybe a short canter to break it up. But that's only after you do all the ground work and ring work to get him some basic muscle tone and a topline.
Ride him up and down hills, in sand if you can, and when working him in an arena or round pen lots of tight turns, he will start to look like he is loosing weight because he will be losing the fat and gaining muscle, so when you start working him hard you may want to increase his feed a bit.
Lots of ground work! Start slow ... Lots of walking and trotting, especially up and down hills and in sand. I think trail rides are great for fitting up a horse that has been out of work for a while. there are lots of obstacles, different types of footing, hills, etc. And it can be a little more lax for both of you.
Lots and lots of trotting. Over poles and on the flat. Do circles and straight lines. Go up and down hills. When you're riding him don't let him just plod along. Make him use his hind end and extend and collect at the trot . This will help build muscle and his movement will be better.
you could try tying a big size tire on a rope and if you have a western saddle just tie the other end to the horn and make him pull it.
hacking out is very good, trot poles are good too.
First of all if he hasn't been ridden in that long a time then you need to start him off gradually. No work in deep sand nor sharp turns, or you'll risk tendon damage. Longeing at walk and easy trot and eventually limited canter is a good start, but not exceeding 15 or 20 minutes per side (with plenty of walking). Then add in some mounted work (depending on how much you weigh) begining at the walk then add the trot, then add the canter, all on the flat with good firm but not hard footing. You can then add work in sand, add hill work or cavaletti or cross poles, but not all at once , and increase the amount of time you're on his back from 20 minutes on up. Start with 3 days per week and gradually work up to 6 days/week.
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As for the exercises, all of the lateral work will be good, starting in walk, then trot then later on in the canter. This type of program will allow you to condition (strengthen) him without risking injury. Depending on how unfit he is (and it sounds like he's very unfit, unless he's very active in the paddock) this will take between 8 weeks to 6 months depending on how fit he needs to be (what discipline and level he'll be competing in).