When Queen Bea tries to seduce Secret Squirrel into doing her bidding, he breaks the curse by beating her love with his hate. It was a defining moment for the series, and it is amazing the writers were able to get away with it, even in the more lenient 1990s.
His fight with One Ton, an endangered panda. He was asked by Da Chief to not harm his opponent, which led to him getting his ass kicked. After a few losses, he figures out a working strategy - he sits on top of the panda's head, not doing anything, nonchalantly jumping out of the way every time One Ton takes a swing, while he beats himself up. One Ton finally decides to smash him with a car, which, of course, just ends with One Ton knocked out. Then Secret takes One Ton to prison for harming an endangered species.
Secret giving Quark one epic Villainous Breakdown. He points out that quarks are hypothetical, telling the subatomic psycho that he doesn’t exist. The result? Boom!