This is going to be a long post, but it's a summary of all the research I've done on "portable" or do-it-yourself training systems. Let the information overload begin.
I'll try to break it down into different training modalities. Nothing says you can't combine this stuff, either. The best routine is one that works for you right now, with what you have wherever you're at.
Barstar / pseudo gymnastic route
The bulk of your workouts are going to require a pull up bar. I have found the most affordable, portable, durable, and collapsible pullup bar that exists on the market. It is freestanding, can handle 350 lbs of weight, constructed of solid aluminum, weighs 22 lbs, and tears down in a matter of seconds into a small duffel. Basic models start at 200 dollars (that's the one I have). The 250 dollar one is a good value for the money because it has bars that you can do dips off of, but I'd rather not have to constantly adjust the height of the pull up bar to do dips every time I want to do dips. I'll use two chairs or a pair of gymnastic rings instead.
Here's the pull up bar.
http://trapezerigging.com/collections/fr...ullup-bars
A good starter routine would be the Armstrong Pullup program. It's already been talked about in the thread, but hey, it works. A good plan today is better than a perfect plan tomorrow, and as a bonus you could easily make it part of your morning routine. In the past it's taken me from 4 pullups to 12 in the span of about 7 weeks. Here's a good website that advertises the effects of the armstrong pull up program. It's no bodybuilding program, but it's better than nothing and it takes very little time.
http://harrycloudfoot.com/2012/05/11/sel...n-6-weeks/
Other good resources would be the websites and forums of barstar athletes.
http://www.madbarz.com/
http://bar-barians.forumotions.net/
The bar athletes tend to do some ridiculous volume, hundreds of pullups every workout and all kinds of variations of pullups, dips, pushups, and maybe some handstand work or leg work thrown in.
If you want a taste of gymnastics and to develop some serious upper body pulling and pressing power, the old Coach Sommers article on the planche and front lever is an excellent minimalistic resource. You could do that program and the armstrong pullup program for a relatively complete upper body workout that takes very little time and only a pullupbar and some floor space.
http://www.dragondoor.com/articles/build...ditioning/
In order to take your training to the next level, buy the Foundation One and Handstand One course on the gymnastic bodies website. You'll have to buy/build more equipment than a pullup bar, but there's a whole entire forum full of other guys just like you who have found out substitutes for equipment or how to build your own. Coach Sommer's program will provide you with a much more complete physical development than doing a shitload of pullups and dips. I do foundation one and I can say that it is both effective and humbling. Foundation One is gymnastics training so yes, the bulk of your training will be upper body or core oriented, but it also has a bodyweight squat series that works well.
Convict conditioning is not a bad way to go, but the volume is far too low and many of the progressions are contrived and an utter waste of time (like those goofy squats where one ankle rolls on a basketball). A better resource would be Al Kavadlo's Raising the Bar and Pushing the Limits! . You'll get an introduction to some different bodyweight exercises with some fairly decent guidelines on how to work up to them and you won't get the ridiculous amount of bullshit that's in convict conditioning.
Calisthenics books written by Ross Enamait are excellent. The Underground Guide to Warrior Fitness is an oldie, but a goodie. Never Gymless is the newer version of that book and it is also gold. You can't go wrong with Ross, although his forum is not the best place to go for fitness advice.
I've heard good things about You Are Your Own Gym, but I've never tried it. I did read the book, though, and just about everything you do in that book for exercises you can do in a hotel room with chairs, a door frame, and a phone book.
As far as calisthenics are concerned, your lower body will suffer. To combat this, you'll have to learn how to do the one legged squat so you can build up your legs to an adequate size. Once you're comfortable doing a one legged squat, you can start to add weight. How you do this is up to you, you can shoulder something, pick up a heavy backpack in your hands or even a rock. Anything will work.
Another way to develop strong legs is to do leap training. You can start with bodyweight squats, work up to bodyweight jump squats for height, then for distance, then add weight and repeat. Building the Gymnastic Body by Coach Sommers is a good resource on this.
The Kettlebeller Route
Kettlebells are basically a cannonball with a handle. They're fairly expensive and they don't go up in weight in small increments. However, they have one huge advantage over calisthenics, and that is you'll be able to adequately work out your posterior chain with basic kettlebell movements like swings, snatches, and cleans. Nothing says you can't do calisthenics and kettlebells, they complement each other well. You also don't need a lot of space to work out with (a small patch of floor in your basement will do) and you can even do your workouts outside if you don't mind your neighbors giving you funny looks. Eminently portable, a set of kettlebells will deliver a fairly complete package for all around physical fitness.
The bad thing about kettlebells is that anything you can do with a kettlebell, you can do with other equipment that is either cheaper or more convenient.
This T handle for swings is more convenient to go up in weight and costs 10 dollars (not including the plates).
and a 20 dollar sandbag sandbag for cleans, curls, presses, snatches, rows, and weighted one legged squats does everything else.
There is nothing unique or special about "kettlebell training".
If you do decide to train with kettlebells, there are some major advantages.
1)Once you have dropped a couple hundred bucks on them, that's it. You don't need any fancy equipment. You might need a place to do pullups, but other than that, you're set.
2) They don't take up much space. Four or five different sized kettlebells are going to take up a lot less space in your basement or garage than a set of barbells, a power rack, a bench, and an olympic lifting platform.
3) Kettlebells are really hard to break.
4) The exercises you can do with a kettlebell are basically swings, cleans, snatches, presses, and weighted one legged squats with the kb in the clean position. Those exercises will give you a fairly complete physical development provided you bust your ass at them. There's also a lot of awkward dumbbell-like shit you can do with them, like curls and rows. A set of kettlebells don't beat a gym membership, but they're a good investment if you travel or you live in the middle of nowhere.
A good place to buy kettlebells would be from the International Kettlebell and Fitness Federation website. Really, any place with good reviews for their products and a standard size of kettlebell will work.
http://www.ikff.net/index.html?page=shop....t&Itemid=6
The biggest reason is that they are all exactly the same size. You don't need to relearn your cleaning, snatching, or pressing form every time you go up in weight like you would with the "russian" kettlebells off dragon door.
A good resource to learn how to use your kettlebells would be Enter the Kettlebell by Pavel Tsatsouline. You can get it off the dragondoor website, just don't get sucked into buying all of their overpriced books. I haven't done much research about kb training other than what Pavel has written, so you'll have to do your own research to find what works for you.
The next topic I would do would be odd object lifting, but I'm pretty sure that if you're just working out at home, you don't have the kind of place where you'd have lifting stones, anvils, logs, or barrels full of gravel.
If you're looking for cheap weight though, sandbag lifting is a good way to go. The definitive guide to sandbag lifting would be Ross Enamait's sandbag lifting DVD titled Low Tech High Effect Sandbag Training. A 20 dollar sandbag and some time to make smaller bags of sand to fit into the larger bag will last you a long time.
As far as effective workout routines with absolutely no equipment, The Naked Warrior by Pavel Tsatsouline is a good read. Spoiler alert, the exercises in there are only the one armed pushup and the one legged squat. I would add in the one armed chin up, but that's just me.
Really, just pick a training modality (calisthenics, whatever) and bust your ass at it every day.