Particle density - Checking this flag will result in certain calculations being performed to determine the total number of particles allowed at any one time.  Basically, it will produce more particles than the max particles value for large generation entities and less for small generation entities.  This tends to cause more realistic particle numbers than trying to figure out a number on your own.

Fade in - Checking this flag means that the particle will generate with an alpha of zero and increase to the value set in Particle max alpha over its lifetime.  This causes the particle to become more opaque until it dies.  Note: this flag does not work with particles with infinite lifetimes.

Fade out - Checking this flag means that the particle will generate with an alpha equal to the value set in Particle max alpha and will decrease to zero over its lifetime.  This causes the particle to become more transparent until it dies.  Note: this flag does not work with particles with infinite lifetimes.  Also note: Checking both fade in and fade out will cause the particle to fade in for the first half of its lifetime and fade out for the second half of its lifetime.

Use world grav - Checking this flag means that particles in your system will be subject to the gravity settings.  This means that particles will constantly accelerate downwards during their lifetimes.

Tri, not quads - Checking this flag will help alleviate performance issues by using triangles instead of quadrilaterals.  Basically, it will help make the system run more smoothly on lower-end computers with a small loss in quality.

Constrain pitch - Checking this flag means that the particle will not orient vertically to correspond with the player's view.  Normally sprites will rotate so that the player sees them directly.  Checking this means that they will only rotate along the horizontal, and not vertically.  This is basically so the commander won't end up seeing sprites at a weird angle, such as fire sprites.

Collide - Checking this flag means that the particle will die when it collides with an object in the world.  This means that particles that hit the wall will die.  This flag will tend to protect your particles from traveling through the void and into a room that they shouldn't be in.  Note:  For generate system on collision to work, this flag must be checked.

High-detail only - Checking this flag means that this particle system is not "essential to gameplay," and will therefore only be drawn for players who have selected the option to have these particle systems drawn.  Basically, checking this flag will help speed up performance for older systems (which likely won't have the high detail option on) by not drawing this particle system.