Shuriken, Kunai, Smoke Bombs, and other thrown weapons
Used by nearly all ninja, Shuriken, Kunai and the like refer to the huge variety of basic thrown objects used by your average ninja. These can vary in many ways, 4, 6, or 8 point Shuriken are all common, as are handled, unhandled, or double bladed Kunai. More advanced ninjas can attach tags or wire to them for sneakier tricks. Some ninja will also carry huge, very aerodynamic Shuriken, that usually fly slower but hit a lot harder. The Fuuma Shuriken or Windmill Shuriken is also often used, a compact Shuriken that can be stowed away in a weapons kit and unfolded for throwing.
Swords, Staves, and other hand-held weapons
Although most ninja in hand to hand combat use their fists and feet, some ninja use swords, spears, staves, brass knuckles, or a large variety of physical weapons. These can be used with specialty Jutsu for a variety of results, but do not always give an obvious combat bonus, and are not always used.
Tags
The "exploding tag" is a very commonly used weapon in Naruto, being a piece of paper that is sticky on one end, and has an explosion seal on the other. Once stuck or tied to a target it works as a time bomb, and can be applied to a Shuriken for added punch, or put on the ground or an obstacle to create a trap. Other tags can create flashes of light, puffs of poison, or a variety of different effects.
Wire
Another ninja staple, Wire is used in a variety of very imaginative ways. Grappling hooks, attaching to Kunai, creating traps, etc etc etc. Another thing no ninja leaves home without.
Weapons kits
The standard Konoha garb contains a pair of pouches, containing approximately 20 Shuriken, 8 Kunai, a dozen yards of wire, and 8 tags of varying types. Ninjas on missions usually carry a backpack in addition, carrying food and sleeping materials, but also a med kit and a single windmill shuriken. Finally, Chuunin and Jounin carry armored vests, which have breast pouches for carrying up to six scrolls of varying types.
Weapon Scrolls
It's very, very common for a ninja that specializes in weapon use to carry a scroll with a lot of weapon summoning seals on it, to quickly access more weapons than they can physically carry. Puppeteers use scrolls to carry their puppets, sometimes weapon scrolls can be used in attacks, etc etc. Touching the correct seal makes the weapon you want appear, and scrolls can carry dozens of weapons. These items are usually only available to Chuunin and higher rank ninja, although ninja that specialize in their use may have access to them earlier.
Summoning Contract Scrolls
In order to be able to actually summon a creature with the Kyuuchiyose ability, you must first sign your name in blood on that creature family's Contract scroll. There is only one contract scroll for each family, and while the Hokage holds the Monkey summoning scroll deep inside Konoha, many are extremely difficult to find. Having a Summoning Contract Scroll on hand gives you a mystical +1 Ninjutsu when using Kyuuchiyose to summon that type of animal, in addition.
Jutsu Scrolls
Much like weapon scrolls, you can store a particular Jutsu inside a scroll for single time use. This can suppliment a ninja in the field, or be used to create strange, combination attacks, such as Kakashi's Doton: Tsuiga no Kyuuchiyose. Chakra is still expended in the normal way, it just allows the ninja to perform a Jutsu they do not know, without the hand seals. It is very rare to see a ninja of a lower rank than Chuunin with these, as they are difficult to make.
Med kits and antidotes
When going on field missions, ninja teams may be given emergency medical supplies for use in the field. These can vary quite a bit in size and use, but as a general rule, will heal one point of maximum stamina damage to each ninja in the squad at the end of the mission. The higher ranking your team is and the more dangerous the mission, the more likely you'll be sent with medical equipment.
Soldier pills
Normally used by the Inuzuka family for use with their Ninja Dogs and Beast Form skill, Soldier Pills are pills containing a huge amount of protein and vitamins, to give boosts to ones energy. They're hard to make however, and only get handed out on an as-needed basis. Eating a soldier pill cures 5 temporary stamina.
Akimichi family pills
The Akimichi family has a special recipe on the soldier pill, that they turn into three pills that will rapidly burn the calories and chakra stores of the user to increase their performance. Dubbed the Green "Wasabi" pill, the Yellow "Garlic" pill and the Red "Pepper" pill, each increases abilities by a certain amount, but at a large loss to the ninjas health. An Akimichi family secret, finding a non Akimichi in posession of these pills is extremely rare.
For game use, eating the green pill in combat will add +1 to Taijutsu, Ninjutsu and Genjutsu for that combat, but reduce the users max stamina by 10 at the end of the combat. The effects of the Yellow and Red pills are similarly cumuilative. The Yellow pill will give +2 Tai/Gen/Ninjutsu for 20 max stamina, and the Red +3/3/3 for 30 max stamina. If multiple pills are eaten in one combat the effects are -not- cumulative, the effect of the strongest pill eaten will be portrayed.
Kusanagi
A legendary sword of an extremely high level of craftsmanship, Kusanagi is the sword of Orochimaru, and gives him quite an advantage in close combat. Using Physique Modification he carries it inside his body, ejecting it from his mouth and wielding it when necessary. In addition to being ridiculously sharp, it can be telekinetically controlled by him, and the natural magical ability of it grants him +1 Taijutsu while he wields it.
Diamond Eight Point Staff
A sort of a combination weapon, this is formed by having the Hokage use the Henge jutsu on the Monkey God King, Enma. Forming him into a ridiculous staff, the Hokage's close combat power becomes much greater. The staff can extend or contract to virtually any technique, is hard enough to break most of anything, and Enma can move his body parts independantly of acting as the staff, reaching an arm out to punch an opponent the Hokage may miss. In addition, the magical ability of the staff grants the Hokage +1 Taijutsu while he wields it.
Sasori's Parents Puppets
The beginning puppets of Chiiyo, they were made by Sasori, modelled after his dead parents. They contain razor sharp wire in their fingers that they can attach between their hands for very deadly pincer attacks, and each contain a variety of poisoned weapons in their upper arms, needle shooters in their mouths, and can form both of their arms together into a Chakra shield.
