I recently upgraded a couple of sites to EE2.5.5. I was utilizing templates to store JQuery and its plugins, combining all within an index file of my 'scripts' group. This isn't necessarily best practice, or how I typically include JQuery in my more recent builds, but it worked for the sites for a very long time. Upon completing the EE2 upgrade, JQuery included in a template produces a script error, breaking the site's scripting.
Here is an example error from firebug using JQuery 1.7.1:
SyntaxError: unterminated string literal ...entElement;q.setAttribute("className","t"),q.innerHTML="<link/><table></table><
This occurs on all versions of JQuery I've tried, minified or not, and produces a variety of errors.