"Chakra Training"
There are several different ways ninja are trained to learn to better use their Chakra. For each of these ways that have currently been revealed, we have given an explanation of what it is.
Tree Climbing: In this exercise, the user must gather Chakra at the bottoms of the feet, and then walk up a tree as if it were ground. If you have gathered too much Chakra you will break the tree and be thrown in the opposite direction. With too little Chakra, you will also fall. However, with the correct amount the user will actually stick to the tree. But, this is just the first step. Doing this for a matter of seconds is the "easy" part, sustaining it for minutes, or even hours is the true test.
Kakashi believed if his students could sustain it long enough to walk to the top of a tree they had learned this exercise and passed the test. Being able to do this successfully is a big step in learning to properly control and manipulate ones own Chakra.
Water Walking: Similar to Tree Climbing, think of this exercise as merely a more advanced version of the same thing. Like the Tree Climbing exercise, the goal is to gain better control and manipulation of one's own Chakra. Also like the Tree Climbing exercise, producing too much or too little Chakra will result in falling. The user must produce (and sustain), just the right amount of Chakra.
Unlike the Tree Climbing exercise, what you're walking on isn't a solid surface and is constantly moving! This means that exact amount of Chakra you need to produce is different then when on a solid surface, and may be different from time to time. When this is taught to Naruto, an extra part of the Kyubi seal is removed, giving Naruto much less restricted Chakra flow.
Leaf Concentration A related training exercise to Chakra Molding, Leaf Concentration will hone a Ninja's concentration ability. Therefore, only those who have worked hard at their ability to concentrate can become excellent Ninja. For generations Konoha ninja have practiced their concentration, and have used the Leaf Concentration exercise. To keep the mind from becoming distracted, a leaf is placed on the user's forehead to focus upon.
As explained by Naruto's early teacher Iruka in a flashback, the leaf emblem on the Konoha head protectors comes from this exercise. Iruka liked this exercise, and tried to show it to Naruto and three of his other students when he saw them having trouble concentrating. While trying to master the Rasengan Naruto thinks back to that lesson, and uses Iruka's advice help complete the 2nd stage in learning the Rasengan.
Sources: Naruto Episode #10, Naruto Episode #53, and Naruto Episode #88