In Episode 7, Goemon cuts two missiles cleanly in half mid-air, thus preventing World War III from breaking out and resetting the metaphorical doomsday clock. Out of all the awesome things he's done in the Lupin series, this might very well take the cake.
Goemon Ishikawa XIII vs. Daisuke Jigen in the last two episodes. Just as awesome as it sounds.
Fujiko overcoming her demons in the final episode and completing the act by delivering a "The Reason You Suck" Speech to Aisha's mother masquerading as the late Almeida.
Fujiko: You just stood back and watched while your daughter was being tyrannized. You're no mother to her. All you did was mess up the tale of Aisha's life. You couldn't even let her keep a reminder of her kind mother.