There are a legion of different routines and workout plans that are calisthenics based, but this is what I do.
Lower body (Monday and Thursday)
I. Jumping squats and walking lunges superset, 4 sets
-If you are wanting to produce muscle you really need to push the muscle to it maximum, so you'll have to really jump. Just getting some airtime isn't enough, you have to jump on each repetition to your maximum, and then go right into the walking lunges.
II. Jumping squats and side to side lunges, 4 sets
-same thing, just a variation on the lunges.
III. sprints (at least 5 sets)
-I sprint the length of a soccer field. Again, an all out sprint, not just a fast run.
Upper body (Tuesday and Friday)
With upper body I do the same basic idea of supersets, but there is a lot more variety in the exercises you have available to you.
I. Wide grip pull ups (palms away) and dip super sets (3 sets)
-I use gymnastics rings for the dips on one of these days just to get a variation.
II. close grip chin ups (palms facing you) with pushups (feet elevated) superset (3 sets)
III. Ring pull ups with your palms facing one another and diamond pushups (your hands will be touching and making a diamond) (3 sets)
IV. Body weight rows (again, I use gymnastics rings for this workout and am in a laying position pull my self up with my feet remaining on the ground. Pulling the area below my chest up towards the rings.) Do this with wide grip push ups (on the pushups, go down towards one hand and pushup, and then go down towards the other hand.) (3 sets)
V. upside down hanging shrugs (rings are best, but you can also use a bar. Hand upside down and shrug to work your traps), and body weight skull crunchers (I don't know how to describe this one, so good luck.
Some of these workouts I have posted at my youtube page which is below, you should check it out. I'll be posting better routines in the near future.