I'll keep this simple - predicated on you only needing to stop for a night or two. For those who really want to go overboard, check out Graves' book. The guy even has instructions for making coat hangers! It's a shame about his passing, he was an Australian bush icon, and he certainly knew his stuff.
Camp site selection
At the broader scale, where you camp is dictated by your planned route. Needless to say, it is in your best interests to plan your night-locations to be somewhere reasonably sheltered from the elements and preferably close to water. Consider natural hazards. For example, the base of a cliff may be nice and sheltered. It could also be subject to rockfall. Branches and coconuts can fall from trees, snowdrifts or avalanche could hit. Pessimism can be a bit of a downer, but looking at the worst-possible-case could save some pain later. Just don't dwell on it too much or you'll never sleep.
One characteristic of a night-loc I consider to be important is to have a few escape routes, with planned alternate rendezvous points for night-locs. This is not just a military thing. In some places there are natural hazards where you may have to quickly bug out. In bushfire-prone areas, you may have to exit very quickly. Flash floods can occur in river plains.
At the finer scale, consider the micro-terrain. Gullies are sheltered with trees, but they are cooler and, gravity being what it is, more prone to water running through them. Are you on a mini water-course or in a depression that could become a swimming pool? Are you exposed to the wind? Wind can be bad (cold), but a wee breeze can cool you in hot climates and keep mosquitoes away. In snow, lee sides are sheltered (good) but prone to accumulating drifts during snowfall (bad). All this being said, use natural shelter when you can. Even if you are in a tent, convenient fallen trees or dense bushes can help shelter from wind and driving rain. If you are just in a tarpaulin or bivi-bag, local vegetation is even more useful for guying your tarp.
Don't forget to think about what's underneath you as well. Soft, springy vegetation is comfortable and provides insulation. However leeches also like those places too. Nice clear gravelly patches may look good to camp out on. But in Australia and southern Africa they are indicators of ant colonies. There is no hard and fast rules to selecting a patch - you need to use some observation, think things through and learn the lessons as they occur.
Proximity to water is good for resupply, but notwithstanding the flooding hazard be aware of any other hazards particular to the area. Animals are attracted to water points. Other water sources, particularly in northern Australia, and southern tropical Africa are home to river geckos, snapping handbags - crocodiles. It pays not to be too close to them. Mosquitos and sandflies also love the water.
Admin and ablutions
When you are by yourself or in a small group, keeping things organised around you is easier. I have to admit I hate camping in proximity with others. This is not antisociality (well, maybe a little bit), but folks seem to be a bit more self-absorbed and inconsiderate these days. I prefer to crawl off and hide somewhere.
If you plan to have an open fire, prepare the area properly. Clear an area of flammable materials about 1m radius. Try to place it so that prevailing winds don't blow sparks into the flammable areas or indeed into your tent. A ring of stones around it helps define the fire area. When you have finished, make sure it is extinguished properly with water. Don't just bury it. Organic material can catch fire and smoulder underground. Keep it as small as possible for your purposes.
Personally I'm not a big fan of going bush and lighting fires. Yes, they may be nice and cosy but it seems to defeat the purpose of the hippy zen thing of experiencing the bush for what it is. It's up to you though if you want a fire, your game boy, and satellite dish TV. I'll just move somewhere quieter.
In general, if you have sealed food packets such as cans, foil-sealed, or vacuum packed foods they are not in much danger from curious animals if kept out of sight. This however can change if you handle the packets with food-covered hands and put a scent on them. Fresh or preserved foods such as smallgoods are a different issue. The consequences of having these in your proximity varies on the beasties that occur around you.
Rats and racoons can be annoying, cunning, and rats in particular can chew their way into your stuff if they get a scent. This is a bummer. If you are in bear country, having nice smelly food around you can be downright dangerous and in many bear-prone places it is mandatory to carry bear cans. These are a nuisance. It's not the bear's fault - it's those pain-in-the-ass people who insist on feeding them because it looks cute. Unless you are in polar bear country, in which case a nice warm human in a tent is kind of like a wonton.
Fabric food safes are available. Or, in the poor-person's case, a hessian sack does the same job. These (like bear cans) are hung from a convenient tree to at least keep the vermin away from you. Food safes are not rodent proof - rats can climb to them and chew through you and eat your chorizo and limburger stash. But at least they are less likely to chew through your tent, if using one, or pack and spare underwear to eat your food. Bear cans will pick up food scent from you handling it, so it may not be totally effective at hiding food. They have their detractors - usually based on the (correct) premise that if you are off the beaten track, away from those who like feeding wildlife, and are disciplined with your campsite then they are generally not needed. As an aside, to a bear toothpaste and soap is close enough to food to be interesting. These need to be kept secured as well.
If you are in particularly notorious bear or other scavenger (dingos, wolves, hyenas and so on) country and do not intend to spend more than one night, consider getting meal-time out of the way before moving to your tent site. This is an Army SOP - eat, then move to where you will sleep. It is also espoused by Ray Jardine amongst others in bear country as part of the stealth camping philosophy.
While sealed food packets are easier to hide, garbage is more difficult to conceal. I've said this repeatedly - leave no trace. We don't do the bash-burn-bury approach. OK, this is one thing I do get a bit fussed about. Feeding animals and leaving trace are big no-nos in my book. If you are taking fresh food out bush - eat everything. Don't leave the hard broccoli stems behind - eat them. If you are reluctant to eat things like banana peels or apple cores (I eat the cores...) - carry them out. NEVER throw anything with seeds away. The last thing purists like me want to see when in the wild is someone's accidentally-seeded papaya tree. It offends the ecologist in me.
My approach is to dry-wipe any used food containers, such as cans, as best as I can (usually with dirt), flatten, then stow them in a hessian sack. I usually bungee the sack to the outside of my pack. That way if a rat wants to chew through, I'm only down a sack. If pests are a real nuisance, then hang the sack in a tree at night. From experience, my pack is usually so close to me the most I've ever had is a curious rat and the odd racoon sniffing when I'm asleep.
Latrines should be organised downhill and preferably downwind from your campsite and well away from any water sources. If you are in the wild with a larger group, it will be necessary to dig a trench to keep everything in one place. If you don't, you may end up digging up someone elses, well, you know what. These should be covered with a thin layer of soil after each contribution. What a nice word! Kind of like 'an exchange of gunfire'. Sounds all Xmassy. Needless to say, completely cover when you are ready to move on.
At an individual level, I prefer to keep a small trowel in my kit and make a hole as required. For all you dirty smelly boys out there - not everyone appreciates you coating trees in urine. Try and be discreet. Digging a wee hole (geddit?) is more considerate for others.
The rule is simple - leave no sign. Ensure fires are out, pits are covered over, garbage is picked up - basically put stuff back where you found it. Easy.