My list, based upon usefulness along with overall application in the general philosophy of Smash is as follows, but not in any order:
Diddy Kong's banana's are very effective as they do decent damage but have a tripping property. Combined with the Banana Smash Deploy method, an aspect of mind games come into play. You can pick them up with your dash attack and the frusterating using of them will weed out the n00bs.
Toon Link's and Link's bomb are also great projectiles as well. Many techniques have been found to exploit the system and glitch the situations accordingly. However, damage, knock back, and just plain annoyance alone ranks the bombs used by the duo very high. They also have wicked nice smoke effects.
Mario's FLUDD is possibly one of the best projectiles in the game. It does no damage but it can, single handedly, gimp an opponent completely. No other projectile can do such thing consistantly. Yet, the best part is the applications of the technique. It can stop, push back your opponenent, stall your own momentum, and even push your own character back. For a game in which people ***** about mind games and easiness, they refuse to experiment and utilize such an attack. It will take a while before this attack is to be glitched and really put to work. I'm not sure if Squirtle's watergun is is the same, for I have not used it so I won't include it.
Finally, I hold Yoshi's egg toss in high esteem for it is very versatile and can be used to pull off extreme maneuvers. In the air, it can help you recover to the edge while clearing out the edge guarders or huggers. Then, you can do a recovery attack or jump down and Dair then recover, or anything else. That use alone is very good. But also, it is very disruptive and has very little lag and high damage and decent knock back. Furthermore, the mind game situations and chances it presents are truely amazing.
As a last note, I also hold Thunder Jolt, Ice Block, Hand Grenades, Waddle Dee Toss, and the blasters as some of the best however, I decided to write about the projectiles people see as a misconceived waste.