Clearview and neutered interstate shields are too obvious, so I won't include them. However here are some other pet peeves...
-Off centered text. It gets annoying when you see one control city way off to the left or right of the sign. Here is an example:

-Lack of direction on a route shield on a BGS. Signs on the Pennsylvania Turnpike and the New York Thruway have a few interstates that end at them, and they don't even bother to post what direction the interstate is going.
-Obvious green-outs. Seeing signs with a control city covered up with a color patch that doesn't match the color of the rest of the sign. At least try to make it the same color.
-Signs mounted low to the ground on a multi-lane highway. If you are in the left lane, and there is a car to your right blocking the sign, there is trouble. A lot of the Atlantic City Expressway signs have this problem.
-Off standard font on a road sign. Seeing helvetica or arial on a road sign makes me cringe.
-Non-cutout interstate shields. *cough* Rhode Island *cough*. Bubble shields are also a pet peeve.
-Misuse of the new fluorescent yellow/green sheeting on warning signs.

Notice the sign to the left.