Eywa is the guiding force and deity of Pandora and the Na'vi. The Na'vi believe that Eywa acts to keep the ecosystem of Pandora in perfect equilibrium. It is sometimes theorized by human scientists that all living things on Pandora connect to Eywa through a system of neuro-conductive antennae; this often explains why Na'vi can mount their direhorse or mountain banshee steeds and ride them immediately without going through the necessary steps required to domesticate such wild animals.
In Na'vi Mythology
Some believe that this interconnectedness, which on Earth is merely a spiritual concept, exists in a physical and tangible way on Pandora, in the form of a strange, collective psionic consciousness embedded in the planet, drawn from all Pandoran life. It is, in a way, a little like a huge biological internet; the trees being computer servers that store information. The Na'vi can upload or download memories from it using their queues and it can even be used for mind transfers in certain cases.
The Tree of Souls grants the Na'vi access to the psychic essences of their deceased, which is how the Na'vi communicate with their ancestors. The roots of the trees are capable of extending above the ground and connecting to the nervous system of any living thing, even humans. This is how Jake Sully's consciousness was transferred to his avatar permanently.
Avatar: The Game
In the Avatar video game, this psionic link can be manipulated by humans as well. If the player chooses to side with the RDA, then the main objective throughout the game is to gather three psionic crystals in certain areas and plant them near specific crystal willow trees, which are said to be where emanations of Eywa concentrate. This is done so that the willow trees resonate with the cystal's combined vibrations, forming a 'song'. The songs collected from each willow tree can then be used to locate the long-lost Well of Souls. This allows RDA scientists to both find the Well of Souls and build an artificial psionic machine that emulates an aggressive version of the smaller willow trees' signals, which is then planted in front of the active Well of Souls. This allows the RDA to tap into Eywa itself, control the psionic consciousness, and take control of the moon itself to turn it against the Na'vi, thereby giving the RDA a decisive advantage. Eventually, the RDA is successful in these efforts, and is inevitably on the way to winning the war against the Na'vi and taking absolute control of Pandora. This only occurs if the player sides with the RDA.
In Avatar: The Game, the Na'vi can ride and control creatures, like the direhorse or the ikran. The mighty thanator can also be ridden. However, the player does so without connecting to them physically, the way they do in the Avatar film - because the game does not display animated queues for the Na'vi characters. The in-game Na'vi characters, including the player, do have queues, but all are shown to be firmly fixed to their shoulders rather than the free-hanging braided queues visible in the movie. The Dunia engine does support the relevant dynamics, but the system was unused.
In the DS version, Eywa selected Nok to be the Alaksi Nari or 'ready eye'. It was Nok's duty to collect information about the human threat for Eywa, and make her understand that they were a terrible risk to the entire ecosystem. She responded by unlocked vegetal chests and providing Nok with weapons.