My gosh! That's a tough one since I've seen so many series in my time. Well, let me give this a try:
Male: Alucard (Hellsing)
I love vampire anime and probably have every series, OVA and movie about bloodsuckers in my library, and Alucard is far and away the biggest, the baddest, the nastiest and the meanest of the bunch, whether he's whacking other vamps with those insanely huge handguns of his or making fun of his undead flunky Seras Victoria (a.k.a. "Police Girl"). Alucard is death on wheels, and mondo cool! And while most folks here despise English dubbing, Crispin Freeman who voices Alucard provides just the right sort of menace and creepiness that's perfect for the man in red!
Female: Major Motoko Kusanagi (Ghost in the Shell)
This was even tougher since a good 90 percent of my anime collection features female protagonists, featuring everything from superheroines, witches, spellcasters, mecha pilots, cops, space pirates, android maids, you name it, but the Major stands head and shoulders over the rest. Besides being a no-nonsense, badass cyborg, she takes no prisoners and does whatever she has to do to get the job done. Unlike most anime heroines, there's no angst or wimpiness when it comes to the Major, she'll just barge in and kick ***, no questions asked! And she's a babe to boot!