I thought of another. The Judge battle from XII:TZA. Mainly because it not lets you battle all the judges including Drace and Zargabaath, but it also raised their stats for true end game and transformed them into the fearsome force the plot tries to pitch them as but the gameplay fails to live up to.

I also love the Enuo optional fight in FFV. While I generally dislike the new classes, the super dungeon was a very nice addition, and I appreciate it having a small bit of narrative to it.