I hear this as a issue for a lot of companies. Yes Microsoft has some great products for virtualizing old applications, But here some special. UniBrows is a add on for IE8 or IE9 that add a Tab in your browser that allow you to run IE-6 dependent web application unmodified in IE8 or IE9.
This solution work for those customers who need JUST browser backward compatibility. The cool thing about this add-on is that now you can migrate to Windows 7 easily.
UniBrows provides full IE6 functionality and behaviors, including ActiveX controls support and JavaScript functionality. Administrator-specified sites are rendered as if IE6 was powering the separate tab while other websites and nonconfigured URIs are loaded natively in IE8. The add-on can be deployed with standard IT methods, managed by Group Policy within IE8 (so company IT administrators can choose IE6-specific sites and applications to render as IE6), and also includes a Microsoft Management Console snap-in. In contrast to heavyweight virtualization-based mechanisms, UniBrows only requires 10MB of memory without changing a single line of code.
You can even had different version of Java running in your browser!
For a Trial Version go Here