I would have to say
Flash - Nerfed like crazy even in his own show. But I blame the writers/budget for not having enough creative stories so that we really see all the crazy stuff he can do
Deathstroke - Would be #1 if not for Flash. He's been crapped on in almost every form of media. Arrow Slade was great but short******d. Oh, he was cool in Flashpoint Paradox as well.
Dr.Destiny - His appearance in JLU was a complete joke.
Bronze Tiger - Just like Deathstroke, Oliver Queen beat him fairly easily in Arrow every time.
Deadshot - None of them got it right. Arrow was the closest. He was a wimp in Batman: Gotham Knights anime.
Martian Manhunter - Again, nerfed. But at least they got his personality right.
Superman - This is a tricky one, but I think they play him too safe in other media.
The Rogues - For obvious reasons, they never had a chance to be anything but filler villains.