Ok, I am not an expert on ninjitsu. I have compiled here some information I have found on this subject from different websites and other sources. I hope this might be made a sticky. Please you are more than welcome to correct me.
Nin-jitsu was developed during a war by helpless farmer families trying to defend themselves from enemy samurai. This later developed into many different types of nin-jitsu, each with its own special properties.
These family unique types sometimes combined, so that one family would change their name and they would combine their secrets. They started to build villages hidden in mountains, often very hard to reach so that ninjas could live normal lives without having to be on their guard 24/7. Ninjas were normally trained from birth during this period. 1-8 they would start to play games having to do with balance, flexibilty, strength, etc.
9-14, they would work on the actual fighting style, kicks, punches, locks, vital points. They also learned a very interestingly true ability. They were taught to distance run through trees, as in jump from branch to branch. And finally, 15-18 they would learn psychology, so they could predict enemy's movements/thoughts, etc.
Poisons were very popular among assassin ninjas. They were less messy than stabbing the victim or using some other means. They could use the simplest organic sources for poisons. Some examples are:
Tomato & Rhubarb leaves- Caused cardiac problems and eventually cardiac arrest. (Yeah I know, better watch the kids

)
Common Fruit (i.e. apple seeds, plum seeds, cherry seeds, etc.)- Cyanide could be extracted from this and dropped in someone's cup, or be used to coat a dagger or sword.
Scorpions and Spiders- Not only could they extract the poison, but easily drop them in the seat or bed of a target.
794-1192 A.D.- Wealthy families fighting with each other in attempts to destroy or create emporers. Assassins were greatly needed, this allowed the ninja to flourish.
Ninpo- "Ninjutsu is best described as the collection of skills utilized by the Ninja while Ninpo, often referred to as "the higher order of Ninjutsu, " implies a philosophy for living based on the principles of Nin.
Nin translates into patience, but can also imply perseverance, or stealth. The Japanese character for Nin consists of two parts or radicals. The upper radical is called yaiba which refers to the cutting edge of a blade. The lower radical can be read either as kokoro or shin, both of which mean heart.
The character po, which implies natural law, is used rather than do (i.e.. judo, kendo, aikido,etc). Referring to our art as Ninpo rather than Ninjutsu stresses training which is concerned with the internal development of the individual's character along with the technical skills of martial training. It isn't enough just to know techniques, it is where your heart and spirit are as a person that is important. For this reason, Ninpo stresses philosophic and spiritual training in conjunction with the physical training. This refinement of one's spirit is known in Japanese as seishinteki kyoyo.
Ninpo is concerned with the defense of the whole self, and recognizes that defense against a life-threat is dealt with by the spirit as much as with physical technique."
Taijutsu- The ninja's main fighting art- Used normal punches (With some special fists) and kicks, along with pressure point manipulation the ninja was a master of bare-handed combat
The ninja also used many weapons including the: Bo (Staff), Bow (Log ad Short bows), Bokken (Wooden Sword) Chigiriki (2 foot long stick attached to a 2 1/2 long chain attached to a ball with spikes on the end), Darts (Often poisoned), Fukiya (Blow gun used to blow the darts), Naginata (long staff with blade on the end), Kama (Sickle, usually used 2 at a time), Neko-Te (Iron fingernails), Ono (Battle Axe), Shuriken (Throwing stars/other pieces of metal), Sword (About 24 inches, for stabbing), Tessen (Fan), Tetsu Bishi (Calthrops), Kunai (Short kives often used for short range combat and for throwing).
And finally, Ninja Hand Signs:
Kuji-in-
"Kuji-in is the spiritual and mental strength the ninja possessed in the form of hand signs. These hand signs were believed to be able to channel energy. The hand signs were taken from the practices of the early Buddhists.
The Kuji-in was used to build confidence and strength in the ninja. It was also believed to enhance the senses of danger and foresee death for the ninja.
In Kuji-in the thumb represents the source of power (Ku), and the fingers represent the four elemental manifestations. They are Chi (earth - solids), Sui (water - liquids), Ka (fire - combustion) and Fu (wind - gases).
There are 81 hand symbols, total, but there are 9 primary ones: Rin, Hei, Toh, Sha, Kai, Jin, Retsu, Zai, and Zen. Each symbol invokes different strengths and abilities in a trained ninja. Rin brings strength to the mind and body; Hei generates psychic power in order to mask one's presence; Toh enables the ninja to reach a balance between the solid and liquid states of the body, which leads to a greater harmony with the universe; Sha is used to heal oneself or another; Kai gives complete control over the body's functions, enabling one to slow the heart rate, endure extreme heat and cold, etc. Jin increases the mind's telepathic powers, giving a highly trained Ninja the ability to read the character of another; Retsu gives telekinetic powers, enabling a ninja to stun an opponent with a shout or touch. Zai extends the harmony gained by merging with the universe. Zen brings enlightenment and understanding. These symbols take an entire lifetime to truly master."
I will edit this in the future from replies and new information.