I have this book about body conditioning for MMA.
A lot of it deals with body weight training. Let me get some examples:
for some abdominal exercises:
Rock Back: It's like a crunch but you bring your knees up toward your chin while keeping your head steady and a few inches off the floor.
Leg Lift: Lay on your back with you hands under your butt palm facing down. Keep your legs straight and lift them up, then tuck the knees, then extend the legs vertically, tuck the knees, and extend back out, keeping them a few inches off the floor the entire time. Make sure you keep your head off the floor.
Flutter Kick: It starts out like Leg Lifts but you don't tuck your knees, just flutter your legs. Let them get up to about 2 feet off the floor, then drop down to about 6 inches, and raise the other one. Do these somewhat fast, and make sure your head stays off the ground.
Crossed Leg Reach: Sit like you would in a Sit-Up position and instead of doing sit-ups reach your right arm across to the left side of your body, then go down, then repeat on the other side.
Legs:
Squat: Stand up and squat down until your butt is almost the same height off the ground as your heels. There are different levels of squat though. You can go down to where your butt is just half way or a quarter of the way down as well. Then there's the jumping squat. Where you jump forward a few feet land and squat, then jump backwards, land and squat, etc.
Upper Body:
Tricep Dips: Push yourself up by your triceps. This could be between two bars elevated off the ground, or in a kind of reverse push up position where your butt is facing the ground.
Push Ups: There are lots of variations from the standard, to the extra wide or extra narrow hand placements. Diamond push ups where you place your hands in a diamond position on the floor and try and bring your nose in the center of your hands.
There's the Dive Bomber push up: Your hands should be about as wide as a standard push up, and your feet about about 2 feet apart, then you place your butt in the air so your body is doing this big inverted V. Then sweep your body until your back is arched downward and your head is facing the sky. Then reverse the sweeping motion until you are back to the starting position. These are very similar to the Hindu Push ups that were mentioned earlier.
Pull ups/Chin ups: Pull up is when your palms are facing away from you, chin ups are when they are facing towards you.
There's also an entire guide thats meant for building up explosiveness/agility that works your quick twitch muscle fibers. But that should be good just for getting into shape using your body weight only.