great topic, no easy answers. there is no clear cut winner. here are my picks in no particular order; i think any of these i feel could be arguably called the best, and my reasons why:
sheeva's fireball. the strongest projectile by far (12%, 16% enhanced) hits mid/overhead, large hitbox, armored when EN, and has extreme knock-back if used as AA or if EN;
shang tsung's ground skulls. excellent recovery, extremely versatile. can be used close, mid, or far, for zoning, offense, and defense. juggles opponents for horrendously damaging, un-breakable combos. shang's viability as a character, period, revolves around this projectile.
noob saibot shadow charge. amazing speed, amazing start-up and recovery times. hits mid/overhead. fast enough to be used naked even at close range.
kabal's gas blast. speedy, good damage, ridiculously great recovery time. can be used on ground or mid air for ia attacks.
kabal's buzz saw. like the gas blast, has almost unfair speed and recovery. also fast enough to use naked at close range. one of the few projectiles that can be used as a truly reliable wake-up attack;
kitana's fan throw. fast projectile with good recovery and start-up times. can be used for ground or in mid-air. can start, continue, or finish a combo. EN is cancelable and has extreme recovery/speed. the key ingredient for kitana's most destructive combos, and the bread and butter of her entire offense.
freddy's glove toss. so very fast, such enviable recovery and start-up. EN is very damaging. all of freddy's projectiles are superb, but this IMO is his best.
sindel's air fireball. the best projectile from one of the best zoners in the game. speedy, quick recovery, and the bane of all non-teleporting characters. a clean counter to so many attacks.
sindel's low fireball. like kabal's buzz saw, very rare in that it is a projectile that's an effective wake-up tool and can be used naked at close range relatively safely. allows sindel to duck and avoid most other projectiles while using it. when EN, it floors an opponent, and is very damaging.
ermac'c forceball: underrated projectile which is deceptively fast, recovers speedily, and (i believe) can't be ducked due to it's unusually low trajectory.
stryker's gun shot. impossibly fast, can juggle effectively, and can be dash-cancelled. dangerous at any range. too fast for any high or mid-hitting projectiles to trade with it.