Tetsu-Bishi (calthrops) - small metal weapons shaped so that one point is always up. They, like the shuriken, were a weapon used for distraction while fleeing. The ninja would scatter the calthrops behind them and anyone unlucky enough to step on them would not likely continue with the pursuit. They could also be thrown, and dipped in poison like the shuriken.
http://hirschls.com/WebRoot/Store27/Shops/52017020-bd8e-4513-b618-75f7e492391b/5482/32E1/0E36/2177/1619/0A48/3570/41AE/IMG_4176_m.JPG
Photo reference for Tetsu-Bishi/Calthrops, found on Google Images.
Tanto - The tanto, or knife, was an important weapon in the ninja's arsenal. Like the ninja-to, the tanto was not made of the high quality steel that the samurai's sword was but the ninja made up for this by using the tanto as a multi-purpose tool.
The tanto was used to pry open doors, dig holes or small ditches, or it could be thrown like a shuriken. Of course, the tanto was also used to cut and stab an opponent as well.
http://www.meismartialarts.com/images/Products/Daggers/S-237BR.jpg
Photo reference for Trypp's Tanto, but only the blade itself. Credit unknown, found on Google Images.
http://www.meismartialarts.com/images/Products/Daggers/S-237BK.jpg
Photo reference for the sheath of Trypp's Tanto.Credit unknown, found on Google Images.
Poisons - Ratsbane, organic and easily accessible poisons from the seeds of fruit (i.e. cherry, plum, apple, peach.) i.e. Cyanide. A mixture of tomato and rhubarb leaves resulting in cardiac arrest. "Amanita phalloides", a deadly mushroom, easily slipped into meals and only takes a small piece to cause certain death. Either dipping his Fukiya darts in the concoctions or slipping them into the food unsuspected.
Not all of his poisons are meant to kill, some are used to paralyze, cause temporary blindness, or put the victim to sleep.
http://orig10.deviantart.net/db60/f/2006/332/7/5/texture___ratsbane_by_markopolio_stock.jpg
Ratsbane. To be crushed and drained of the oil of the leaves, put into a vial.
http://www.discoverlife.org/IM/I_MWS/0293/320/Amanita_phalloides,I_MWS29302.jpg
Amanita Phalloides. Either a small piece broken off and put into the meal of the enemy, or crushed and squeezed of oils for his darts.
https://followthelemur.files.wordpress.com/2012/11/cyanide.jpg
Cyanide, typically accumulated by the seeds of particular fruits or bought through trusted associates. The latter being very few and far in between.