Warning: This page contains theoretical information based on the research and speculation of one or several other users. It has not been officially verified by Nintendo and its factual accuracy can be disputed.
KongsDonkey Kong Jr., his father, and recessive genes from an unknown female monkey for a mother. Funky's involvement in the war could be the reason why he has various types of weapons for sale and has different ammo for each of the said weapons.
Commander Cranky Kong
Cranky Kong was the main Commander and Lead Organizer of the Ape Alliance. Though his loss against Stanley the Bugman shattered his hopes and dreams, The Great Ape War is likely what took the biggest toll on his health, giving him a hunchback and requiring a cane to walk. It is assumed that Cranky was still in top shape during the war, as he brought it to an end after defeating General Krusha in a final battle.
Donkey Kong Jr. likely fought in The War in order to keep his family safe. It is thought that his disappearance in the games is linked to the war. It's unknown if DK Jr. survived the war or simply disappeared. Fans theorize that a mysterious unused Kong character wearing a fedora could be a disguised Jr.
General Klump was the lead pilot of the Kroc-Army during the war. Klump is responsible for shooting down the Biplane Barrel, piloted by Funky, resulting in the loss of his tail.
General Krusha was the most formidable soldier in the Kroc-Army, which contrasted greatly with his low intelligence. He would often be sent on reconnaissance missions to retrieve the Crystal Coconut from the Primate Alliance, failing every time. His climactic showdown against Cranky Kong ended the war.
In the days of the war, K. Rool was not the leader of the Kroc-Army but a high-ranking Commander (it is unknown who he succeeded afterwards). K. Rool is responsible for ordering both Generals Klump and Krusha on various missions which almost always failed.
Mr. X may have been the leader of the Kroc-Army during the war but at some point he was assassinated and becomes the undead ghost skeleton known as Kackle.
Manky Kong Betrayal
When the future was looking bleak for the Primate Alliance, certain groups started questioning whether the war could truly be won. One specific group, the Manky Kongs, began to prioritize the survival of their kind alone, resulting in a rebellion against the Primate Alliance. The Alliance did not forgive them for this and the Manky race remained Kong Family rejects throughout history. While uncertain, it is speculated something similar may have happened with the Minkeys.
It is unknown how Lanky Kong, being a reject orangutan, was accepted into the Kong Family later on. It's possible that he was too young to be involved in the betrayal, or he was more close with the main family of Kongs.