The one where you had to generate and dynamically size and position an iframe underneath any draggable element that might end up on top of a select. I personally wrote a couple of fixes for that, and there were many more.
IE5's interpretation of the CSS box model, where border and padding are included as part of the element width (now available everywhere as box-sizing: border-box). It makes more sense in a lot of cases, but good luck getting your design to look right across browsers without strange incantations like "width: 495px; wi\dth: 500px".
My personal favorite is when console was undefined if devtools wasn't opened, making a simple console.log call crash the script.