Values listed in brackets are for alternate (secondary) fire.
One of the most powerful weapons in the game, the M99 has very high damage (the highest of any bullet-type damage in the game), a decent head damage multiplier, and nearly unlimited bullet penetration. Its drawbacks however are its high cost and limited ammunition, as well as the long (~4 second) reload time.
Aiming for the head is a good idea since it will double your damage.
Try to line up enemies to take advantage of the penetration. Hitting 4 enemies in the body means the first will take 675 damage, the next will take 506 damage, the next will take 379 damage, and finally the fourth will take 284 damage, equating to over 1800 damage for a single bullet.