The Empress of Time in Warrior Within. Even on Easy, it took me replaying the game and making sure I got all the health upgrades just to have barely enough life to beat her. At the end of the fight, I was out of sands and the sliver of health I had left was so small that I couldn't even see it anymore. Again, this was on Easy with all available health upgrades until that point.
Essentially, the fight is just a one-on-one sword fight. Like most bosses, you are limited in the acrobatics you can do. Trying to climb over her will cause her to knock you down, and she sometimes will even move out of the way of attacks launched from a wall or a pillar. This mostly limits you to using basic attacks and sand powers, but the problem with adding those sand powers is that she not only is the only boss that is partially immune to them (ex. she can still block to some extent if you slow down time), but it also reduces the number of times you can rewind time if you get killed. Oh, and you can't replenish them, considering the minions she summons a couple times never drop any.
After that, she is just incredibly unforgiving. Attack too many times, she'll block and launch a quick counterattack that will possibly knock you down. Block for too long and she'll go low, knocking you down. She may also teleport right behind you, and if you try to dodge the inevitable attack the wrong way, The Prince will end up trying to climb over her which, as I've already said, causes her to knock you down. Oh, and she also doesn't have any qualms with striking you a couple times while you get up, and as I'm sure I've made clear, getting knocked down is a common result of even minor mistakes. The fight isn't necessarily unfair outside of the occasional control problems all the Prince of Persia games have, but it is really unforgiving and probably the last time a boss really challenged me to an excessive degree.
With that said, I've never been more thrilled to beat a boss, and I'd even say that that fight is among the most enjoyable boss battles I've had. Sure, it made me rage quit multiple times and even got me to restart a game I wasn't particularly fond of at the time. However, I still haven't found a major sword fight quite as thrilling as that one.