Bit of an odd choice, but I always found that Shredder from the first Teenage Mutant Ninja Turtles worked really well, making a one-shot character from the comics, and more of a comic buffoon from the TV series into a genuinely evil and intimidating antagonist. Looking back on the film, some his stuff descends into cliche at times, but its still a strong performance.
The thing I love in the ending is that the film really builds up the Turtles as fighters, then have the big face-off with Shredder... and he just wipes the floor with them in the fight. Takes his time, waits for them to plan, and still just takes them out easily. It leads to a solid ending though with Splinter essentially goading him into self-destruction, and Casey Jones doing the finishing touches. In hindsight they would have better off leaving him dead, and going with another villain for the sequel.