This one seems like a no-brainer, but it had several of our best JS experts stumped for a good while, until we saw what was right in front of us all along.
A script for preloading images was failing. The source was similar to this (imagine 20 or more lines of unbroken script):
Notice how the first line of script is preceded by an HTML comment delimiter. This prevented the
preload_images function from running, as the JS interpreter just skipped over the entire line. For the want of a linebreak, the script was hosed.