I've got a lot of favorites. Depends on what you're looking for in a character. I still maintain the best character in anime that exemplifies manliness is fucking Kenpachi.
Though, Spike from Cowboy Bebop was pretty awesome, even if his last two episodes got a little...I dunno...they felt a little emo to me.
Also Wolf's Rain entire cast of male characters had surprising depth for an anime I...didn't think I'd like.
Its a toss up between a few really
Grell Sutcliff (Kuroshitsuji)
Alois Trancy (Monoshitsuji)
Crona (Soul Eater)*If you believe Crona is a boy
Gaara of the Sand (Naruto)
Suigetsu (Naruto Shippuden)
Akito/Agito Wanjiyama (Air Gear) *Might have mispelt his last name
Sooo hard to choose, but favorite? No! I'd still have to top 4 it...
Akira Kaburagi Regendorf from Dance in the Vampire Bund
Spoiler:
He's a good man and will always try to do what's right, but he loves his princess and wants to stay with her forever. Plus he's a werewolf in love with a vampire why not; he goes from emo to badass in two seconds flat.
Alucard from Hellsing Ultimate
Spoiler:
He's cool, he's powerful, and he's stylish; he's not a man, he's a monster... but I'd take a monster like him over most men any day ;)
Roy Mustang from Full Metal Alchemist
Spoiler:
He's got a commanding presence, the vision to want to make the world a better place... and he's hot hot hot - especially when he's angry.
Touga from Utena
Spoiler:
Redhaired sexy master swordsman who loves to leave his shirt open. He knows all the cliche lines and can deliver them with expert timing. It's true you wouldn't be the only girl he saw that day, but honestly that sexy he had to be a player.