Java and JavaScript have almost nothing to do with one another. Java is a full-featured computer programming language. With it, programmers can create entire applications and those applications must first be translated into machine code that the computer's CPU can understand. However, Java's main use in a browser is to create applets, which are small programs that download over the Internet. Java applets are embedded into Web pages using the HTML <applet> tag, and when a browser sees that tag, it downloads the applet from the server, and runs it in the browser in an area of the screen specified by the applet.
On the other hand, JavaScript doesn't have to be translated into machine code first to be understood. When a browser sees the HTML <script> tag, it simply checks to see which language the script is written in (i.e JavaScript, VBScript, etc.) and your browser is able to take care of things from there all on its own.
The JIT compliler in IE does not need to be enabled for IE to understand JavaScript. And in fact, unless you regularly visit Web sites that use applets, I wouldn't even enable it. If, however, you do visit sites that use applets, I would suggest that you set IE's Virtual Machine security to high. To do this, first select "Internet Options" from IE's "Tools" drop-down menu. From there select the "Security" tab, highlight "Internet" and click on "Custom Level...". Scroll down to "Microsoft VM" and click on "High safety". (It's perfectly fine if the custom settings itself is set to "medium".) Then clck "OK".