Anime with MC being very strong, unbeatable (at least not in the main plot or important fights), and badass.

Mondaiji-tachi ga Isekai kara Kuru Sou Desu Yo? *
Kaze no Stigma *
Hagure Yuusha no Estetica *
Mahouka Koukou no Rettousei *
Hidan no Aria
Code:Breaker
Sword Art Online (MC is very strong but he's not as badass as the ones mentioned before)
Campione!
Toaru Majutsu no Index
Blood Lad
Btooom!
Ichiban Ushiro no Daimaou *

Animes with MC being very smart, and badass

Death Note
Hyouka *
No Game No Life *
Log Horizon

Manga with awesome, powerfull, incredible, badass, and/or smart MC

The Breaker Manhwa *
Tora Kiss *
Wolf Guy (18+)
Witch Hunter *
Naruto (I know, but you should check the manga if you don't think Naruto should be in this list)
Kurogane (Kezawa Haruto)(awesome power and ability, but he's not that badass)
Koe no Katachi (Not powerfull or incredible, i mean, is a love story so... But MC is badass an awesome in his own way, you should check this one)
Iris Zero *
Defense Devil *
Beelzebub
Aiki