1. Son Goku
This choice might risk being cliche, and it's certainly tempting to think of Goku as the "Japanese Superman" and focus on his immense strength. However, this doesn't do the hero of the Dragon Ball saga justice. Throughout his many adventures, Goku was a fighter that never backed down and always put up a serious fight whether he was overmatched, equaled, or clearly superior to his opponent. He was once a youth that fought just about all of his future allies at least once, earning their friendship or at least respecting in return. This could never have been accomplished with strength alone, which Goku had from the beginning of Dragon Ball. He also learned much about the art of fighting from many different teachers, destined to surpass them all in time.
In the Dragon Ball Z series, he fought an incredible variety of powerful and skilled opponents over time and proved his worth against each one time and again. Take for instance his battle against the Cell, who Goku was able to hold his own against despite the villain knowing just about every technique that he and his friends did. Goku didn't win every battle he fought, but he could be counted on to come back for more and show remarkable perseverance.
2. KenshiroKenshiro from Fist of the North Star was inspired by the examples of martial arts legend Bruce Lee and Max Rockatansky from Mad Max. Kenshiro was pretty much overkill personified. This man does not defeat his opponents. He dominates them, and he mostly does it with raw strength and his martial arts skills instead of energy blasts that blow apart the landscape. He does this through his fictional Chinese art Hokuto Shinken, wherein the martial artist destroys or manipulates his foe by striking his acupressure points.
Some of his abilities are powerful enough to destroy limbs, some are actually subtle enough to affect the nervous system and make the opponent's body act involuntarily. Incapacitation, decapacitation, and even gruesome outright destruction often befall Kenshiro's foes; no defense is safe against his flurry of fists. Woe upon the post-apocalyptic tyrants and thugs who challenge him.
3. BatmanBatman is one of the most capable American superheroes, and he isn't super. He is a man that pushes his considerable talents as far as he can make them go. Interestingly enough, the nature of Batman's martial arts prowess has been subject to revision over the years. It's probably easiest to concur with the general consensus of comic book writers these days, which holds that Batman has studied just about every type of martial art worth knowing and is able to effectively use their techniques as needed.
All this is fine and Batman does have plenty of useful tools and gadgets as well, but as any serious fan would agree Batman's greatest skills are his wits and intelligence. Batman also excels at thinking on his feet and predicting what actions his foes will take next before they do them. In short, Batman excels at fighting on his terms in a way that very few do.
4. The Teenage Mutant Ninja Turtles If nothing else, the TMNT are arguably the most famous martial artists in animation ever since the original 1987 cartoon. They may have arguably started out being best known for "Cowabunga!" and Pizza rather than their fighting prowess, but much has changed since the Turtles first came to television.
In the original comic by Kevin Eastman and Peter Laird, they were hardcore and took no prisoners. When their second cartoon series came along in 2003 from 4kids, much of the fun was kept but inspiration was also taken from the Turtles' comic book origins. It certainly helped that the Turtles were mostly opposed by villains that usually offered a serious fight, including a much meaner and tougher version of the Shredder. This trend continued in very underrated 2007 film TMNT, where the turtles had plenty of slick moves and were perhaps shown at their most ninja-like: lithe, agile, skilled, and more than capable at striking lethally from the shadows. In their long animated history the TMNT's ninjutsu skills have certainly been tested, and one sure wouldn't want to bet against them in a fight.
5. Spike SpiegelBefore Mugen's improbable breakdancing swordplay in Samurai Champloo, there was Spike's martial arts in Cowboy BeBop. Spike is a user of Jeet Kune Do, a real discipline of martial arts founded by Bruce Lee that calls on the user to use simple, direct movements with a variety of moves from different styles--in short, to practice a style of fighting that defies style and is flexible "like water."
Sure, he carries a trusty sidearm, but when things get up close and personal Spike relies on his considerable skill and finds ways to survive. Given his difficulty against some tougher opponents like Vicious and Vincent Spike isn't quite as superior as other martial artists on this list, but he's got the skill and he's got the style. When Spike is fighting at his best, he makes martial arts look easy and very cool.