Sonic & Knuckles:
(Sonic's story) Death Egg Zone 2 Boss until the end of Doomsday Zone (when you have all 7 Chaos emeralds)
Shenmue II:
Baihu in the cage match, he isn't the final boss, but his best of 3 rounds battle and finale QTE sequence to finish him puts him here.
Street Fighter II (1991)
Four bosses: Balrog, Vega, Sagat and M.Bison in their unselectable form when they were suped up and tougher then their future selectable versions.
MGS3:
Boss. Ah! a Boss who disarms you, joy! When you were able to get the CQC down it created an awesome exchange of counters and you felt the tension when she tried to reverse you then you counter her reversal and ..
MDK2:
Emperor Zizzy Balooba. this jerk was tough and a total ass,, ranks here as one of the tough frustrating bosses,, with a silly sense of humor "curtains! fade to black!"