Canon Weapons

Shuriken
Ninja stars, you have big ones and small ones. With the big ones you can attack a person head on, while the little ones are just for keeping people at bay. Rarely will a shuriken really kill someone. It's sort of a sub weapon which is used to, in most cases, loose enemy pursuers. All ninjas have the small ones, the big ones are used as a main weapon. F.e Mizuki used it in first episode.
Kunai knives
The weapon of choice for most genins, and a good weapon at it. It can be thrown like a shuriken, but can also be used as a close combat weapon. Most ninjas carry more then one of them, and are trained to use the weapon effectively.
Knuckle knives
Sarutobi Asuma uses these. It's a combination between brass knuckles and a knife. Asuma extends his blades using his chakra, and the chakra edges act as hidden weapons. When an enemy misjudges the distance, and can't figure out the secret to Asuma's blades, he will most likely die. It can also act as a defence against swords.
Swords
Though most ninjas rely solely on jutsus and kunai knives. Some use a sword to aid them in their attacks, some use short swords, some use special swords. f.e Gekkou Hayate's katana, Orochimaru's and Sasuke's Kusanagi. More info about these can be found in their character biography.
Bombs
You basically have three types of bombs, smoke bombs, poisonous gas bombs, and light bombs. The smoke bomb is just your ordinary smoke bomb, it's used to conceal yourself, or escape from battle. And of course a poisonous gas bomb releases a poison which is not to be breathed in. While a light bomb is used to blind a person, just look at it like a flash grenade.
Exploding tags
Pieces of paper with the Japanese character 'Baku', which means 'explode' written on top it. Usually goes at the end of a kunai knife, and blows up after a certain amount of time. But these tags can be placed as easily on any other item.
Medical and poison needles
Thin needles can be used for medical purposes, acupuncture to be more exactly. But just as easy as it can be used as an offence weapon. You can just throw them, or use some kind of needle launcher like Shizune. Shizune even launches poision tipped needles at her opponent. Besides Shizune Haku seems the only one to use them. She creates them from water, and controls them using her advanced bloodline.
Puppets
The idea of using puppets in battle was developed in the Hidden Sand Village. Puppeteer ninjas use chakra strings from their fingers to their puppets to operate them. The puppet itself can be upgraded with many weapons and tools. In most cases the puppet master remains hidden while the puppet moves and attacks the target. Kankurou and Chiyo use them, but Sasori takes it to a new level. Read more about it in his character biography.
Fan
A destructive offensive fan which produces high force wind attacks using the user's chakra. It can also be used for people to get airborne, or for defense. It's a good weapon, but it drains a lot of chakra and needs a lot of strength to be properly wielded. Temari is the only known user of this type of weapon.
Gourd
This should hold water, but Gaara has it filled with sand. It's the source to Gaara's strength and techniques. By using his chakra he holds the sand from the gourd, and manipulates it. He can wrap it around an enemy, and then suffocate him or her - create sand bunshins - create sand shurikens etc. It's his on the fly sand, and acts as his backup sand in case he's fighting in an environment that doesn't provide him with sand.
Scrolls
Not only are scrolls useful for taking notes. They can also be used as sealing scrolls, which are used to seal and contain things that might be dangerous. Or as a summoning scroll, which is used by many ninjas to summon creatures or objects. In order to use them it requires some of the summoner's blood.
Staffs / poles
Blunt weapons which are good for deflecting and defending. Only staff so far was the monkey king Enma when he transformed into a diamond-hard pole for the Third. It's the Third Hokage's weapon of choice, and could alter its length and width at will. Ten Ten does summon some Bo staffs using her weapon scroll at some point, but it's just one of the many ninja weapons she summons.
Sonic blasters
Hollow air tubes build into the palms of the user's hands to allow chakra to force out tremendous amounts of sound pressure. Its attacks are strong enough to crack a stone and wipe out everything in its path. Abumi Zaku is the only one we've seen using it so far.
Bells
A genjutsu weapon which makes illusions of the enemy and puts you under high hysteria or hallucinations by hearing its sound. Kin used this weapon to fight Shikamuru in the preliminaries during the chuinin exam.
Broad sword
Zabuza's weapon is much like Cloud's (from Final Fantasy 7) buster sword. A heavy weapon which is able to literally cut almost anything into two. Though it has an immense and brute attacking power, it has the draw back of being heavy and being difficult to carry around all day long.
Samehade
Samehade is the weapon that Hoshigaki Kisame wields. The name means 'Shark Skin', which is ironic as Kisame looks like a shark himself. The blade is not meant to 'Slice', it's meant to 'Shave' people. For that reason it has very sharp fins, and no real blade to actually slice.
Sickle & chain
The sickle & chain is a weapon that is worn by two people. The two are connected by a spiked chain that can quite easily cut anything in two. The chain can be detachted so the users may move father away from each other. And the wielders each wear a large, metal gauntlet with poisonous claws. When using this weapon, you basically try to surround your opponent with the chain, and once your apponent has been trapped, you cut him or her into several pieces.
Warrior pills
Warrior pills are pills which enhance a ninja's abilities. The pills the Akimichi clan and Inuzuka clan use are specialized for just their type of fighting style. The Akimichi clan uses three types of pills, each one having a different effect on the user. But each one causing immense stress on the body, it's possible to die from taking one too many. The Inuzuka clan uses pills to enhance their smell or merge with their particular animal, such as dogs or wolfs.
Gamabunta's daggers
Gamabunta has two daggers, they are quite strong, and bigger than some of the tallest trees. We've see him using the daggers during the Sannin battle, and in Naruto's fight against Gaara fully transformed.