Also Doom isn't really a hero. Nor is Hulk and Sentry..I guess sometimes he is.
But anyways, I will mention Superman. I like the part in the JLU cartoon where Captain Atom confronts Superman and Supes tells him to step aside and he says no. Then Huntress is all "um SUPERMAN just told you to step the f*ck aside".
I guess not exactly fear. Though from the JL cartoon the look on Kalibak's face is priceless when he realizes Batman wasn't trying to fight him and was just stalling until Superman got there. To which then Superman one shots him.
Though of course the best example of this with Superman is when he confronts "The Elite" and has people thinking he has turned evil and murdered everyone. Pretty much everyone(not just the villains) collectively shits their pants at that point.
YouTube video
It's pretty telling that Superman can come off as more frightening then legit villains.