Transitions, climbing, pole work, half-halts - and lots of them! - just to name a few of the most common ways that fits in any discipline. :)

steady work, starting in walk on the flat, progressing at the horses pace in terms of time ridden & distance covered,progressing to walking up & down hills when they've built up some strength.
When you've got a basic level of fitness, add some schooling work & trot & canter gradually added when riding out.
keep it all steady as if you rush it, you'll cause injury.

I have nothing to add to the above other than to say lots of longlining rather than single line lunging (a) for all the conformaiton reasons that Monty has given and (b) because you get lovely continuity on the turns which helps promote their athleticism and flexibility. I am always amazed how quickly horses get fit and more muscular - wish it worked for me!! Oh, a thought...Food levels may need monitoring as well as a horse in training may need some adjustment:-)

Thank you everyone for your ideas on how to build muscle. I do have a question about work time. How long should each training or workout session be? (just a general work time)

That depends entirely on your horse.
Age, fitness, intensity of the training session, level of training (young unridden or Grand Prix-ready) and so on.
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A newly backed young horse shouldn't work under rider more than 10-15 min to begin with until the back muscles are strong enough to carry himself and rider for longer periods.
On the lines you can generally work for 20-30 min including warm up and walking off for a start and work your way up to 45-60 min. Watch your horse closely for signs of tiring and how positive he is to the work. Give a young/untrained horse a rest every other day to just play on the field.
It's OK to work up a sweat but they shouldn't be soaked and steaming every day.

Thank Kicki. The horse I am working with is a Thoroughbred, 10 years old. and was a race horse. Last time raced was in 2011. When he was sold he was abused and kept in a small stall and not able to run he is a little under weight to me weighing in at 1,235+/- LBS but has not muscle deffinition.

Hi thunder, as he is an ex racehore presumably being 'converted' to a 'domestic' type need to remember that racehorses work on about 60/40 balance front/back whereas pleasure/competition need to be other way round, hence the need to build up the back end and shift his weight back. Another quirk is that shortening the reins means go faster (not stop!)- I once met someone who could not understand that every time she tried to pull him up he ran faster - very scary she found it! And that also brings up another issue, they do not stop in the conventional sense, after a race they run slowere until they stop naturally rather than being brought to a stop. So all these things have to be taught. Forgive me if I'm telling you stuff you already know but I thought I'd share it all, it was all new to me a few years ago and I found it fascinating and explained a lot about some of the ex racers I have met who are very sore and uncomfortable in their new work.

Hello Vicci, Thank you for posting that information. I did not know that they were worked more on the front then the back, so I will change that. As for the stopping issue, that is something I did know about and am working on very slowly using the videos here along side a trainer with a few years under their saddle then I have. We are working him from a walk and not letting him run for a while. With you posting your comment here, someone else reading this may have not known it and may learn something new. Thats what we are here for.