This was part of my neologism dictionary on DeviantArt, but was really more for personal reference.

Annoyed / Irritated:
Waving head around slowly: Not pleased
Rocking from side to side: Upset, irritated.
Nose flare: Mildly annoyed, silently voicing my opinion on something.
Rubbing feet together: Agitated.
Looking up at sky: Annoyed, awkward.
Grinding teeth: Awkward, nervous.
Dragging feet, misstepping, stomping: Protesting; upset
Face cringing up for seemingly no reason: Remembering something really embarrassing

Distressed:
Hiss from nose: Irritated.
Hiss from mouth: Extremely irritated.
Slamming hand and upper arm on wall repeatedly: Scared, distressed. Can also be a self-injurious behaviour.
Appearing dazed, sitting down: Absence seizure. So far this has only happened once, but I figured if it ever happens again I'll sit down on the ground.
Staring intensely at someone: Anxious, looking for help

Happy:
Rubbing mouth with back of hand: Happy, trying to hide smile
Rubbing mouth with back both hands/wrists: Very happy
Nod or bow: Thank you.
Short shivering fits: Excited; releasing energy

Nervous:
Silent, unmoving / hiding: When in a social situation, sometimes I'll just shut down. I won't say anything and hide. I'll also go silent if I don't want to admit to something yet don't want to lie.
Pacing: Worrying or thinking about something intensely.
Messing with hands, rubbing and scratching face, and moving tongue around: Anxious, nervous.
Stimming: May include messing with hoodie strings, shirts hem, paper scraps, thread, ect.
Constant shivering / quaking: Anxiety
Feigning mental retardation: Sometimes if I find myself in a really awkward situation, I'll act more autistic then I really am, using that as an excuse. This usually leaves me feeling embarrassed and guilty, so I don't often do it.

Self Injurious Behavior (SIB):
Like many kids with Autism, if I get pissed of, I'll often take it out on myself. This includes:
Clawing or scratching the back of my hand
Dragging the back of my hand over a rough surface like a brick wall
Biting my arm
Throwing myself against a wall
Digging my thumbnail into the undersides of my fingers
And in less sever cases, stepping on the side of my foot.

Hand Signs:
Pressing thumb to the underside of middle finger: A sign I believe brings good luck. Often used if I'm in a less then desirable situation.
Waving arms at sides in a figure 8 motion: Trying to cool off / too hot.
Thumb sticking out between index and middle finger: The Fig sign. A sign used in Turkish or Slavic cultures, serving the same purpose as the middle finger.
Hands at sides, flipping hands so palms show: A signal that I don't what to have anything to do with the current situation. I also might do it while passing through a crowd.

Casual / Relaxed
Peeping, guttural sounds.
Making animated facial expressions for seemingly no reason, when I'm talking inside my head.

Other Behaviours:
Knuckle cracking: Bad habit. I do it without thinking.
Swaying side to side: Very uncomfortable.
Kicking item on the ground: When I see something interesting on the ground, like a coin or rock, I might kick it. That buys me time to decide if I want to pick it up or not.
Humming in response to a statement: Either I don't have anything to contribute to the conversation, or I didn't hear what you said.