I've taken a stroll through my tables files and formed a semi complete list of all flags in the game.  Some are blank because I couldn't figure out what the flags do, so if anyone could fill me in on their function and if I'm missing any, please do.  
Weapons Flags
in tech database - probably makes this available in the tech database, one would think.
player allowed - gee, let me think about this one
stream - 
puncture - punches through armor to subsystem
shudder - makes the ship shudder when fired
esuck - I imagine it drains energy from the target, amount unknown
particle spew - 
corkscrew - makes weapon "effect" move around while traveling
EMP - provides EMP effects, screws up the targets systems
Big Ship - I think this make only usuable by big ships, can't be mounted bomber turrets
Huge - 
beam - probably designates it as a beam weapon
supercap - 
Flak - probably has to do with that it explodes when the shells reach thier target.
lockarm - 
Bomber+ - 
Bomb - can be targeted 
Spawn Whatever, # - Creates # of missile type on detonation
Remote Detonate - detonates when fire is pressed again
No Dumbfire - needs lock to fire
child - 
Ship Flags
player ship - 
default_player_ship - used in FRED Teamloadout
fighter - designates as fighter
bomber - designates as bomber
in tech database - appears in tech database
repair_rearm - 
freighter - designates as freighter
cargo - designates as cargo
cruiser - designates as cruiser
gas miner - designates as gas miner
awacs - designates as awacs
capital - designates as capital
big damage - 
corvette - designates as corvette
no_collide - 
navbuoy - designates as navbuoy
drydock - designates as drydock
dont collide invisible -
knossos - designates as knossos
sentrygun - designates as sentrygun
