They get in the way. Do not use frames. Use properly organized navigation aids in place of frames. Pop Ups Anything that pops up is a nuisance. If it is important, put it where it belongs, right on your web page.
Animation can be extremely annoying.
If you must use it, use it sparingly. Have your animation cease after two or three cycles. Just as bad is blinking and scrolling text. Avoid marquees in the bar at the bottom of browsers as well. They do nothing.