My choices won't be popular, but here's what I believe to be the best from all the games I've experienced:
Jedi Knight 3: Jedi Academy = Not so much the singleplayer, but the multiplayer had great physics, allows for pretty much any kind of attack you can concieve of, and rewards player judgement and skill above all else. Brilliant if you like to feel like you are the one making the difference.
Kingdom Hearts (series) = Melee fights straight out of an OTT anime; as epic and sheer fun as you'll ever get, and most importantly, allow a hell of a lot of different choices and approaches in every encounter. At first it can seem fairly average but once the combat 'clicks' you'll be hooked for life.
Dead or Alive (series) = What I would say is the most realistic of all traditional fighting games (to an extent). Where games like Tekken make stringing together some punches more difficult then real life, everything in DoA is context based and extremely fast. Again it rewards judgement and reaction times above others.
Someone mentioned the Onimusha series; While I do not think the combat is the best, it is extremely good at capturing the 'feel' of various styles to good effect. To excel at fighting with the samurai you need to fight like one; to excel at fighting with a western soldier, you need to fight like one. Worth a try if you like a more realistic take on samurai fights: otherwise try Genji for a more cinematic samurai experience.
That is all.