The main divinities that aided the Greeks were Hera and Athena. This goes back to the tradition of the Judgment of Paris, in which the Trojan Paris chose Aphrodite as the most beautiful of the three goddesses. Thus, Hera and Athena, angered at being rejected by this Trojan, decided to help the Greek side in the war.
As for the Trojans, they were supported especially by Aphrodite, who was the mother of Trojan Aeneas, and who was chosen by Paris as the most beautiful goddess in the above-mentioned Judgment. In Iliad 5, Ares supports Aphrodite and ends up getting attacked by the Greek Diomedes. Ares also supports the Trojans in Iliad 20, as do Artemis, Apollo, Leto, and the river Xanthus.
In Iliad 16, we see Apollo helping the Trojans as he prevents Patroclus from scaling Troy's walls. Apollo and Poseidon are said to have built Troy's walls. Poseidon rescues Aeneas from Achilles in Iliad 20, but earlier in the same book Homer says he was going to fight on the Greek side. In Iliad 20, we also hear that Hephaestus and Hermes were going to support the Greeks.
Zeus aids both sides in the war. When asked by Thetis, Zeus agrees to help Achilles. In Iliad 16, however, when Zeus' son Sarpedon, an ally of the Trojans, is about to be killed by Patroclus, Zeus considers rescuing Sarpedon from the battle.