I've never tried to calculate a percentage of compliance or variability of JavaScript across browsers and never seen anyone report it that way. I'm not certain how one would compute such a value meaningfully. However, there are major differences in the implementations of JavaScript between IE and just about everybody else. Most non-IE browsers, e.g., Firefox, Chrome, Opera, Safari, etc., are VERY similar to each other JavaScript-wise. In almost every case that I have branch code for handling things differently in JavaScript, depending on the browser, my comments to detail the branches are simply "IE" and "non-IE" (everybody else).
If you can lay hands on a copy of O'Reilly's "JavaScript: The Definitive Guide" ( http://oreilly.com/catalog/9780596101992/ ), it offers the best presentation of the differences in all aspects across browsers. Base language aspects of syntax are consistent. The prototype OO basis of the language is reliably implemented in the same (apparent) fashion. That's the end of the good news.
Microsoft follows an ENTIRELY different event model than that used in most other browsers. For an online discussion of differences between the event model of IE and that of the more compliant, non-IE browsers, see:
http://www.javascriptkit.com/jsref/event.shtml
The structure of the DOM differs in some pretty extreme ways in IE vs. the rest of the world. Since the DOM differs between IE and others, there are also JavaScript differences related to function and property names. That is, for DOM elements that differ, the properties differ, and hence, the functions by which to access the different elements also vary.
If you're willing to accept the weight (lots of code + steep learning curve) of some of the JavaScript libraries such as the YUI, JQuery, etc., many of the differences are concealed beneath an abstraction layer. This allows you to remain ignorant of the differences, since you call the library functions that "always" work the same in all browsers. Frankly, I prefer knowing the differences, since the libraries are pretty huge - including JavaScript frameworks for trivial purposes is not a bandwidth burden I want to inflict on my visitors or customers. There's also the potential for conflicts between multiple libraries. I've seen huge numbers of question in Y!A and elsewhere along the lines, "I had everthing working with JS_library_X until I needed to add JS_library_Y - now everything's broken...HEEEELP!" Coders who only know the libraries rarely understand how to identify and resolve such errors.
To summarize, there are MANY differences, some huge, others small and insidiously sneaky.