Before we compare and contrast the three systems, let's take a look at what the three represent.
The encomienda system was originally instituted by the Spanish monarchy to exact tribute from its Native American labor force in the Americas. This tribute system was designed to richly reward Spanish soldiers or conquistadors who took charge of Native American tribes. These leaders were granted the right to inculcate in the natives a knowledge of the Spanish language and the Catholic faith as they reaped the results of native labor. For their efforts, they could exact any tribute they desired from the Indians. However, these Spanish leaders had no ownership of the land; they owned only the labor that worked the land.
The repartimiento (literally "partitioning") system was a system of forced labor as well; it was imposed upon the native populations in Spanish America and the Philippines. In this system, natives were forced to work in mines, fields, and in workshops. The Spanish monarchy basically used repartimiento as a means to reward Spanish nobles for their loyalty.
The mita system constituted another system of forced labor; it was imposed upon the Peruvian citizenry by the Inca empire. The mita was essentially a public service system; the government used the workers to complete public construction projects, and many native citizens worked on building the Emperor's monuments, houses, and royal buildings. They also worked in mines and tended communal and royal fields.
The three are similar in that they are all systems of forced labor. However, a major difference lies in the fact that the mita was imposed by an empire upon its own people, while the encomienda and repartimiento were imposed upon native Indian populations by the Spanish crown. While the native Indians had to labor to enrich their foreign overlords (in the encomienda and repartimiento systems), the Peruvian people worked to enrich their society as a whole. The mita was a government tribute system that the Peruvian citizenry participated in; they served as soldiers, farmers, and laborers on behalf of their emperor.
The mita system directly benefited members of the citizenry. For example, when Peruvian soldiers went to war, they could rest in the knowledge that their fields would not be left untended. As a mandatory public service system, the mita required the obligatory participation of all able-bodied individuals once they turned fifteen. All individuals had to work until they reached fifty years of age. However, the mita allowed individuals time to work their own lands as well.
To again reinforce the major difference between the mita and the other two systems, it must be noted that the Spanish eventually co-opted the mita system to serve their own ends. While the original Peruvian mita was instituted for the mutual benefit of all, the Spanish mita was used only to enrich the Spanish crown. During the colonial period, Spanish overlords forced the native Indians to work in the silver mines of Potosi (Bolivia). The toxic gases in the mines and the mercury-infused process of extracting the silver led to millions of native deaths. So, the Spanish-instituted mita was an openly exploitative system.
Often, native Indian populations were forced to use up all the fruits of their labor to pay the tributes they owed to their Spanish overlords. Unlike the original Peruvian mita system, laborers were given no time to work their own lands or to earn incomes separate from work in the mines.
In the meantime, the Spanish encomienda and repartimiento systems led to the advancement of global trade from the 15th to the early 19th century (something the Peruvian mita never did). As time progressed, the Spanish desire to trade with the rest of Europe led to new rules regarding the payment of tributes and new changes regarding agricultural output. The native Indians were forced to pay their tributes in cash instead of commodities, and instead of working mainly the mines, they were forced to produce goods the Spanish considered valuable.
For example, conscripted laborers had to begin producing the cochineal dye in larger quantities because red dye was rising in popularity in Europe. Essentially, the Spanish began forcing the native Indian populations to change their commercial habits to aid Spanish success in the area of global trade. Thus, trade routes that linked the Americas to the Europe were gained through the blood and sweat of millions of Indians.
So, to recap, the encomienda and repartimiento systems were always used to enrich the Spanish crown (whether workers mined for silver or worked to increase the output of commodities favored for trade). On the other hand, the original Peruvian mita was instituted as a public service system to benefit Peruvian society as a whole.
Source: Encomienda and Repartimiento.