Don't parse HTML with regexen! Seriously, it's literally impossible in the general case. Why do you want to use a regex here? It would make much more sense to use an HTML parser, though I can't give you any particular suggestions because I don't know what language you're using. If you're using the JavaScript DOM, for instance, you would want something like the following:
var scripts = document.getElementsByTagName('script')
var numScripts = scripts.length
var textScripts = []
for (var i = 0; i < numScripts; ++i)
if (scripts[i].text !== '') textScripts.push(scripts[i])
This looks at the structure of the HTML to determine the properties of the script tags, rather than at the messy text.
Edit 1: Apparently, you're using Java. Unfortunately, I don't know anything about parsing HTML in Java, so I can't give you any recommendations; however, look into that, because it's the way to go.