The 2000s were a radically different era for action filmmaking, thanks in large part to the modern innovation of the cinematic universe. Before the MCU, the DCEU, the Monsterverse, and the Dark Universe, action movies were free to experiment and innovate with new kinds of antagonists and enemies on the big screen.
After the radical "in your face" atmosphere of the nineties and the hypermasculine action hero fare of the 80s, the 2000s are a slightly strange era for the genre. Dated edgy young adult melodrama would bump shoulders with semi-true historical epic. The 2000s were a weird time, and not every great villain of the period got their time in the sun.
Commodus - Gladiator
Joaquin Phoenix, possibly now best known as the star of Joker, turns in a stellar performance as the nightmarish Roman Emperor Commodus. This classic Ridley Scott period piece combines sobering portrayals of the brutality of the past and well-executed action. Russell Crowe stars as Maximus, but the plot is driven by the scheming monster who seizes the throne. Commodus is the source of all the evil that befalls Maximus. He slaughters his own father, then has Maximus' wife and son brutally murdered, then leaves the warrior for dead. Cruelty is the fire that makes Commodus a threat, but ambition is the most interesting aspect of his character. His lust for power leaves him obsessed with public perception, making him one of the most chilling portrayals of a politician in film history. In every major way, Commodus is perfectly executed.
Girgori Rasputin - Hellboy
Adapted from the Hellboy comics, which, in turn, were adapted from the life of the Russian mystic, the on-screen version of the Mad Monk is a haunting villain. Guillermo del Toro's Hellboy movies are underrated as a whole, but the first film has a far superior villain to the second. Rasputin is a powerful occultist who houses an otherworldly being within him. His attempts to unleash the malevolent beings he serves accidentally result in the appearance of a young Hellboy on Earth. Rasputin wants to free an otherworldly cosmic force that could cause the death of all things, but, after discovering Hellboy, changes his plans. The Mad Monk doesn't seek to defeat the good guy of the film, he seeks to corrupt him. Rasputin's motivations are interesting, and his methods are deeply compelling. The conspiracy-laden narrative makes him historically fascinating and Karel Roden's performance in the role is note-perfect.
Kitano - Battle Royale
Tragically, this 2000 Japanese action/horror epic has been largely reduced to being the namesake for a stunningly popular game genre. With a concept that would later be made world-famous by The Hunger Games, this adaptation of Koushun Takami's novel is a gripping human drama. In a grim near future, the Japanese government has adopted legislation designed to stop teenage delinquency. They intend to keep children in line by choosing one class of middle schoolers, shipping them off to an island, and forcing them to kill each other until one remains.
Kitano is the teacher of the class who, after being injured by a student, nominates his class for the violent lesson. Kitano, named after his portrayer Takeshi Kitano, isn't as sadistic or cruel as one would think. He's indifferent to the death of his students, willing to kill at a moment's notice, and portrayed as put-upon, rather than gleeful for his new position. Takeshi Kitano is an effortlessly charismatic performer, and his stripped-down performance is a perfect embodiment of the banality of evil.
Howard Saint - The Punisher
Jonathan Hensleigh's 2004 take on Frank Castle couldn't be more different from the modern MCU iteration, but it still has its merits. One such merit is the hilariously evil Howard Saint, a violent gangster who feels peeled from the pages of an early Punisher comic. John Travolta can be a difficult actor with a lot of weird roles under his belt, but a scenery-chewing villain is within his comfort zone. Saint is responsible for the death of Castle's family, so The Punisher's vengeance quest seeks to destroy him specifically. The back and forth between Thomas Jane's Castle and Travolta's Saint forego the narrative power of the MCU's Punisher but comes with a different kind of fun. It's hard to imagine any modern action movie bringing out a villain quite like Howard Saint.
Simon Skinner - Hot Fuzz
The big twist at the end of Edgar Wright's beloved deconstruction of American cop movies reveals that almost every character was a villain. The one figure in that crowd that everyone would've seen coming was the unnervingly chipper Simon Skinner. Timothy Dalton's upbeat supermarket manager is one of the most impressively off performances in modern film history. Skinner isn't technically the main villain of the film, but he's the most dangerous, dynamic, and engaging force on-screen at all times. Skinner isn't scary because he might kill someone, all he has to do is smile and make conversation to come across as pure evil.