Donald Pierce is a villainous version in X-Men. He's a bully, and a Dirty Coward, but in a fight he's a match for the likes of Wolverine.
In The Superior Foes of Spider-Man, The Shocker is treated as a coward by his allies due to his unambitious nature and his preference for keeping his head low, even though he happens to be one of the most effective combatants of the team. In his words, he has no problem with others considering him a coward as long as he's able to live another day. Near the end however, events more or less drive him to cut loose, at which point he not only single-handedly defeats the entire team but was also able to defeat The Punisher with a single blast, though exactly how much of this was embellished by Boomerang (who in the end admits that he's making up half of the story) is true.
When he started off, Miles Morales was easily frightened and focused on the negatives, but when needed, he'd go into battle.
Commander Blanx of the pre-Crisis Martian Manhunter comics is a villainous example along the same lines as Donald Pierce. A Dirty Coward and Combat Pragmatist who never fights fair—and indeed, doesn't fight at all if he can get someone else to do the dying for him—he's nevertheless very dangerous when cornered, nearly killing J'onn in one appearance and going toe-to-toe with Superman in another.
The New 52 version of Power Ring is an enormous wuss that seems fearful of everything. However, he wields a Ring of Power that runs on fear which makes him as powerful as the rest of the Crime Syndicate. At least until he ran into a TRUE master of fear.
Kyle Rayner relative to other Green Lanterns. Kyle, unlike all Lanterns who came before him, could actually feel fear and doubted his abilities and heroism frequently. Eventually, his ability to feel fear made him the only lantern capable of spotting the greatest threat to the entire Green Lantern Corps, Parallax. Even Dream of the Endless once told him he'd surpass Hal Jordan because he knew fear.
Jessica Cruz never stops being scared of all the things she has to deal with as a Green Lantern, but her ability to overcome her fear is what makes her one.
In Supergirl story Bizarrogirl, Bizarro and his cousin are biological weapons of mass destruction, but they are quite cowardly. Bizarro wanted to escape from Bizarro World instead of fighting an Eldritch Abomination. Bizarrogirl admits to being terrified of the Godship, yet still does a bang up job fighting it after she grows a spine.
In Archie Comics' Sonic the Hedgehog Mordred Hood, one of Robotnik's minions, is a cowardly and overly cautious guy who would rather keep his head down than fight the heroes. He feels that he isn't cut out for fieldwork, but is actually a surprisingly skilled infiltrator and an intelligent manager, with his cautiousness ensuring that he doesn't recklessly run into danger like some of the other Egg Bosses. The problem is that he's also so much of an Extreme Doormat that no one pays his legitimately good suggestions any mind.
Sonic the Comic portrayed Tails in this light for a lot of the early issues.
Rex and Pugsy in Beasts of Burden. Notable that Rex was a Miles Gloriosus in the first story, but has gotten better. All of the characters are regularly terrified by the supernatural occurences that surround them, but these two (especially Pugsy) are the ones most likely to be visibly afraid—and yet neither will back down when their friends or their town is in danger
Empowered of the comic of the same name is a variation on this—instead of considering herself a coward while still being brave, she lacks in self-confidence in her super-heroing duties while still trying her darndest to be a superheroine—which, as her friends point out, generally ends up demonstrating that she's better at it than she thinks she is.