There are several weapons commonly associated with ninja. The most famous is probably the shuriken, or throwing star. However, shuriken were probably close to useless if you wanted to kill some one. Its shape and size made it difficult to throw accurately and, because it had blades on all sides, putting contact poison on it would be a risky move. Most people agree that it was probably used as a distraction on the rare occasion that a ninja fought. A more lethal weapon would be the kunai, or throwing knife. It was heavy and more accurate than a shuriken and much more to the point.
While the shuriken is one of the most iconic of the tools used by ninja, the ninjato was probably the most useful. Surprisingly, the ninjato was simply a rather small, easy to carry knife. In the rare event that a ninja would have to fight a samurai a smaller blade could be useful, it could be drawn more quickly than a katana (the samurai weapon of choice) and give the ninja a chance to attack before their opponent could strike. Supposedly, these knives were put into scabbards slightly too large for them so that the extra space could be used to store small items that might come in handy. Although I don't agree with claims that the ninjato was the end all be all of ninja weapons, it was undeniably useful.
To a ninja, a weapon was a tool, they didn't treasure them the way samurai did, but it's still hard to imagine a ninja that isn't armed to the teeth with a plethora of exotic weapons. Because they avoided direct conflict, weapons weren't as important to ninja as most people assume, but they've become a part of the westerner's mental image of a ninja.