Learn what the person is like when he isn't talking about anything emotionally charged. This is called the baseline. If you are close friends with someone, you probably already know what his neutral body language is. If you aren't, you can establish a baseline by talking about indifferent things like the weather.
Understand the differences between a fake smile and a real smile. Real smiles involve two muscle groups: the zygomatic major, which pulls up the lips, and the orbicularis oculi, which causes the cheeks to rise and the eye sockets to crinkle. Fake smiles (also known as "business smiles") often involve only the mouth. Also, fake smiles often last longer, while real smiles may only last for half a second.
Watch for distance. When people are comfortable with you, they are likely to stand closer to you than when they are wary. Keep in mind that physical distance can be affected by culture. For example, Mexicans stand closer together when they talk than most other North Americans do. Closeness can also have other meanings besides comfort. Someone trying to dominate you may stand close to intimidate you.
Watch the hands. People unconsciously communicate things they may not want you to know with their hands all the time. For example, if your friend were talking about a mutual friend and said "he does make some people uneasy" while moving her friend towards her chest, it could mean the the mutual friend actually makes her uneasy. Similarly, if a friend is discussing two different options while "weighing" them with her hands, the one that she holds lower is the heavier one--the one that she prefers without necessarily realizing it.
Watch for signs of avoidance. If someone crosses his hands in front of his chest, for example, it might mean that he is "closed" to you or unwilling to hear what you have to say. The same goes for someone leaning away from you while speaking to you or holding his hands up as if pushing you away.
Watch for openness. A relaxed posture and loose and expansive gestures can indicate familiarity and friendliness. Some people also touch people they are talking to when they feel comfortable. Keep in mind that some people simply aren't conversational touchers, so not-touching shouldn't be seen as a necessarily negative thing.
Look for unconscious mirroring. When people are tuned into what you are saying and feel friendly towards you, they will unconsciously sit in a similar style to yours.
Learn to spot contrived gestures. Many people try to consciously adopt gestures to put others at ease as a way to influence them. For example, people who study Neuro-Linguistic Programming (NLP) will consciously try to imitate your posture. Many people actually find this off-putting rather than comforting. If a gesture looks forced, it probably does not convey the speaker's real intentions.