Out of my experience:
Some Games that Deliver on Their Final Bosses
Chrono Trigger
Super Metroid
Final Fantasy VI
Super Mario Galaxy 2
Super Mario Galaxy
The Legend of Zelda: A Link to the Past
Super Mario 64
Metroid Prime
Super Mario World
Super Smash Bros. Melee (assuming event #51 is the final boss)
Some Games that Fall Flat with their Final Bosses
Super Mario Bros. 3
Resident Evil 4
The Legend of Zelda: Twilight Princess
Metroid: Other M (actually, my biggest issue with this game was that the ending seemed like it came too soon)
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Currently Playing - StarCraft: Brood War