Axel from Disgaea 2 is a fallen "Dark Hero", one-man Goldfish Poop Gang and all-around goofball, frequently making up excuses whenever his can gets kicked. However, much like his spiritual predecessor Mid-Boss from the first game, he winds up helping out Adell and company late in the game (but not out of the kindness of his own heart).
Luigi, originally nothing more than a sprite recolor of his older brother, Mario, has slowly developed into one of these.
To say nothing of the Toads: even at his worst, Luigi is still braver than these guys.
Gilgamesh from Final Fantasy V runs away when battles turn against him, generally claiming urgent business has suddenly come up. Later, he does the opposite with a Heroic Sacrifice.
In the sidekick (and mostly comedic) vein, how about Arnaud G. Vasquez from Wild ARMS 4? At one point in game, he actually runs away and cowers behind a box, leaving the rest of the main characters behind. He does get better, in a 'true bravery means working around your fear' way. And by working around your fear, we mean smashing him with a squadron of fighter jets.
Louis from Left 4 Dead. It seems in the Canon, his fear of the infected seems to get him and the rest of the gang in trouble, due to his tendency for flight over fight. Despite this, his ridiculously optimistic attitude and emphatic enthusiasm makes him one of the more entertaining characters for many players.
The first game has poor Khalid, a shy, nervous, but kind-hearted fighter with decent dexterity and at least one-third more hit points than many other party members. Given tons of armor he's a fantastic tank, it's just that he has this tragically low morale score..."Better part of valor! Better part of valor!" In some circumstances this is actually helpful, though, like when he's an inch from death and you can't get a healer into melee to save him.
The Spathi of the Star Control series are like this. Their ship is even designed to fight while running away. It's also one of the more powerful ships in the game.
It's telling that in both the second and third games, when you meet them for the first time, they will immediately surrender and beg for mercy. In the third game, it's because somebody messed with the screen resolution on the Spathi in question's communicator, so he doesn't recognize you at first. However, their technological progress is the direct result of their fear. When a new predator showed up on their homeworld with a taste for Spathi flesh, they went from Stone Age to nuclear power in under a century, all to escape to their moon.
There is a legend among the Spathi about the Black Spathi Squadron, who bravely head straight for danger and fight for justice. Given the nature of the Spathi, they consider these mythical Spathi certifiably insane.
Donald: *Shivers* Goofy: I'm scared too, Donald Sora: Hades, come out!
We later learn that Donald was even more cowardly in his youth, during his Musketeer years.
When they visit Halloweentown again the thing that scares Goofy and Donald the most is the Nightmare Retardant Christmas attire.
Another example of Donald's cowardice is in the manga adaptation, when he accidently grabs onto a Magnum Loader while playing on a Light Cycle, causing it to speed all over the junkyard while refusing to let go, resulting in Sora attacking it head on to save his friend. However, this results in him and Goofy coming close to a Heroic BSOD because the Magnum Loader crashed into Tron during the incident, causing him to drop a crucial piece of data needed to get the trio out of the computer that's imprisoned them; Sora snaps them out of it.
Which is to say nothing of Captain Qwark, especially how he faked his own death in the third game.
There's Dion inTears to Tiara 2, descendent of wise men who only want to be a travelling bard and tries to run away or surrender at the first sign of trouble.
Giving a Sim in The Sims Medieval the "Cowardly" trait essentially turns them into this. They'll be afraid of the dark and a bit of a nervous nelly who talks about their fears to anyone who'll listen, but they don't necessarily screw other Sims over like a Dirty Coward would (except at times when Cruelty Is the Only Option for the player), and they're actually not that ineffective on quests. Even if they're knights.