This question comes up a lot among suppression talk.  The difference between the two types of ammunition is actually not that complicated.  Simply put, if you are going to shoot suppressed, you will want to use subsonic ammo.  Scientifically speaking, subsonic means the projectile is moving slower than the speed of sound.  The actual speed of sound will vary based on temperature and humidity.  In relatively dry air the speed of sound is 1126 feet per second.  Anything under 1126 ft/sec is subsonic.  Supersonic projectiles produce a mini sonic boom which is usually called a sonic crack.  Sonic cracks are not desired by suppressed weapons and they are only masking the bang from the end of the muzzle.  Once the bullet leaves the barrel is begins to produce a loud crack.

Supersonic is anything above 1126 ft/sec such as most 9mm rounds.  Most .45 ACP rounds travel a little over 900 ft/sec making it subsonic by design.  9mm rounds can be purchased in a higher bullet weight (or reloaded) which slow down the projectile to subsonic speed.  This is commonly 147 grain and even 158 grain.  Subsonic ammo will have a slightly different point of impact vs standard 115 grain ammo due to the bullet weight.  Shooters looking for long distance out of subsonic ammo are often disappointed. Here is a look at shooting an MP5 with supersonic 124 grain ammo combined with some 147 grain subsonic:

The .223/5.56 is terrible round for suppression.  By design, the projectile travels so fast (usually between 2,220-3,200 ft/sec) it is nearly impossible to bring them down to subsonic speed.  There are a handful of manufacturers that will use a 100 grain bullet (over the standard 55 grain) and lighten the powder charge.  These rounds are considerably less accurate at distance and usually require an adjustment to the gas system to allow for proper cycling. However, they often must be cycled manually.