Mr. Peg Leg Bat scared me so bad. My bed was by the window and for years I thought he was going to come in and get me. I had to sleep with my parents a lot and also share beds with my brothers. I literally wouldn't go outside when it was dark out for around three or so years after seeing that movie.
Another was The Thief and the Cobbler. The bird scared the crap out of me.
Same thing with Quest for Camelot. The griffin scared me so bad even if it really was a big dolt.
Also Ruldoph's Shiny New Year. Terrible Eon haunted me until I was about 13 (no joke). If I went outside, to play night games with friends, I had to stay within arms reach of someone at all times. This way if Terrible Eon showed up they'd be able to grab onto me and prevent me from being taken by him.
Also Pebbles and the Penguin. The main bad guy was so scary when walking through the stores I couldn't even see a picture on a vhs case without freaking out.
Lets just say that animated birds scared the living daylights out of me as a kid.