Chakra

Essential to even the most basic jutsu, chakra is mixture of the energy present in every cell of the body and the spiritual energy gained from exercise and experience. Once mixed, it can be channeled through the chakra circulatory system, which is to chakra as the regular circulatory system is to blood, to any of the 361 chakra points (called tenketsu) in the body. Through various methods, the most common of which is Hand Seals, the chakra can then be manipulated to create an effect that would not be possible otherwise, such as walking on water.
By mixing different ratios of the two energies, new type of chakra can be formed. The most common product is elemental chakra, which is use to perform elemental jutsus. Most ninja have a natural affinity to one type of chakra, but they have the capacity to create elemental chakra apart from their own affinity. There are six basic elements, each stronger and weaker to another; five have been shown so far, but their relations, weaknesses, and strengths to each other are all explored with the unnamed sixth seemingly skipped. In addition to these six elements, certain Kekkai Genkai can mix elemental chakra to form new elements, such as ice (wind and water) and wood (earth and water). While many ninjas can use more than one type of chakra, they cannot use them simultaneously.
==Normal Chakra==
Normal chakra is a form of energy all individuals naturally produce. Chakra circulates inside the human body, similar to the cardiovascular system, but can also surface outside the body. Normal chakra is not normally visible to the human eye when it is use to perform a jutsu. Chakra is visible in situations where a person is releasing as much of their chakra as possible, though this is rarely seen. Chakra is also visible to do specific jutsus (Kaiten, Rasengan, etc), which take a high degree of chakra control to perform. 
Out of the many different types of jutsus: Ninjutsu, Genjutsu, Doujutsu, and so on, all require the use of chakra. However, Taijutsu is different. It basically requires no chakra use whatsoever. Stamina is all that is needed. While the ninja still needs chakra to live, regular Taijutsu doesn't require any active molding or manipulation of chakra (with few exceptions). A standard attack like a punch or kick falls into this jutsu category.
Chakra is the resulting form of energy when 2 other forms of energy are mixed together. The 2 energies are referred to as "physical energy", which is collected from the body's cells and can be increased through training, stimulants, and exercise, and "spiritual energy", which is derived from the mind's consciousness and can be increased through studying, meditation, and experience. Having these 2 other energies become more powerful will in-turn make the created chakra more powerful. Therefore, practicing a jutsu repeatedly will build-up experience, building up one's spiritual energy, and thus allowing more chakra to be created. As a result, the ninja is able to do that same jutsu with more power. This same cycle applies for physical energy, except this time, instead of doing things like meditation, the ninja could, say, do push-ups. The general term for the source of chakra, the overall physical and spiritual energy a person has, is "total stamina".
Chakra takes time and lots of training to gradually build up. So what's really the key is not actually having chakra, but being able to sufficiently control it. Because, everyone has chakra, but only skilled ninja can correctly "mold" and "manipulate" it to it's fullest extent. 
Molding chakra means to extract energies from both the body's cells and the mind's consciousness, then mixing them together within the individual. The amount of each energy will differ from the type of technique the ninja wishes to execute. In other words, a ninja could create too much or too little chakra for a given jutsu, and the chakra cannot be used effectively. In addition, even if a ninja is able to mold the correct amount of chakra, if they aren't able to manipulate the chakra properly, the technique won't be as effective or not executed at all. Wasting energy will create a weakness of not being able to fight for a long period of time. The general term for the exact molding and manipulation of chakra is "chakra control".
As an in-between stage, some ninjas can partially control their chakra. This means they can use their chakra, but not effectively control it, which results in poorly executed justu, and more importantly, running out of chakra early in a fight. To manipulate their chakra more easily, hand seals can be used. With these hand seals, users can control their chakra with higher efficiency, allowing them to execute their jutsu more effectively. Different jutsus require a different hand seals.
Based on which jutsu the ninja uses, the type and amount of chakra will be different as would the elements you would be to employ. The five main elemental types are also the names for the Five Great Shinobi Nations: Fire, Wind, Lightning, Earth and Water. Each ninja has the potential to better utilize one of these styles and potentially more. A sixth element has been mentioned but has not been revealed. A special elemental detecting paper is used to determine ones type. When the ninja imbues the paper with a portion of their chakra, the paper will alter to reveal one's type. Fire = burn, water = wet, earth = turn to dust, lightning = crumple, wind = cut in half.
== Basic Elemental Chakra ==
The strengths and weaknesses of elemental chakras are as follows: Fire is strong against Wind, Wind is strong against Lightning, Lightning is strong against Earth, Earth is strong against Water, and Water is strong against Fire. Chakra types such as wood and ice are the result of combining different elemental chakra types.