I agree with many of the battles posted, like MGS and Twilight Princess.

From the FF series I would nominate the FFVI final battle, FFVII's Ruby and Emerald Weapon, FFX's Nemesis.

FFXI has it's share of intense battles. Some of the most intense I faced were against Alexander in the Treasures of Aht Urhgan finale, and the airship fight against Omega and Ultima in the Chains of Promathia storyline. That airship battle is widely considered the hardest mission in the entire game due to the 60 level cap and the 45 minute time limit given to win 3 different battles.