Below are some recommended web links that I would definitely give a look over, as well as expansions:
What is Texture? by Rich Burlew is a great introduction on how to get away from cut and paste jigsaw puzzle adventures. When you take on the role of a GM, the entire rest of the party will be relying on you to tell them everything about where they are and what is happening. If all you describe is a 10 foot square room with two orcs guarding a chest, your player will almost invariably picture their own cut and paste, bland, featureless vision of what the scene looks like. Thus, give detail. Tell them about the stink of orc filth and mildew as they approach the room. Let them feel the cold brass of the door covered in orcish warnings to keep out. Describe the the blood encrusted and dirty armor and blades of the hulking scarred orc wariors standing defensively around a red wood and steel chest of elven design marred by orc graffiti depicting the unflattering orc vision of what elf women look like as the players enter the crudely cut granite room, 10 feet square.
Making the Tough Decisions by Rich Burlew is a good first step into having NPCs act in ways that ARE realistic, but do not make sense in game mechanics. For example, while villagers in most games run from the orc murders, DMGII shows us that the typical 3rd level adversarial 20 orc raiding party could be over taken easily if the entire hamlet organized into mobs and wrestled them down. Similarly, there is no good reason in game mechanics for the village maiden to try and sacrifice herself to save her village from the dragon. But these are all good examples of real people doing shit they feel is necessary, even if there are good game reasons not to.
Emotional Responses by Rich Burlew. I know that I have put the pages out of sequence, but for a reason. If the last item was good for jogging you NPCs of game mechanic brains, this is their second step towards making them real people. While not every NPC in your game needs a back story and game stats, they at the very least need feeling to hurt and egos (or lack of one) to stroke. If the Bartender Borg sounds the same as James the Smith who sounds the same as his wife and kids, who somehow sound the same as the orcs that are raiding the village, not only will your adventures be bland and boring outside the dungeon, but NPCs will not matter to the players. And soon you will be running that dreaded game where hirelings are used like clay pigeons with no remorse because they are "just NPCs", and most games with that mentality suck to run.
Villain Workshop by Rich Burlew is not just for villains. I recommend for all NPCs of importance (and players, too) to try using this for making believable characters. And it works. I even know novelists who use a similar method for creating characters, and they come out decent most of the time. This is not a perfect method, and done wrong can produce awful stereotypes and clichés, but for the noob it is invaluable as a starting point.
Dungeonomicon (3.5e Sourcebook)/Socialomicon is a great tool for understanding and creating functional D&D social systems. Before this understanding, a guarantee that all noob GMs in evitably cry when their king of a vast empire is killed by 3rd level characters because they only made him a fourth level aristocrat. I went through this pain at thirteen, many others before me have as well. But you, the ever so insightful newb who wishes to learn (can't even call you noob anymore, because ther is a difference between Newb and Noob.) will not go through this pain.
Now, go forth, and harness thine GMing skills, least ye start a campaign and suffer great pwnage!