SEO and Web Site Code

[EWSitesCom]

I am aware that the search engines like good organized clean code. What if I come across a web site that has unorganized code that is built is aspx with asp includes that cannot be changed. For example. There is a mile long java script towards the top of the web page that covers 142 lines. When I view the code in search simulators it reads the java script. Because of this, the site has lost page rank, and now msn is not picking the site up any longer. I know Yahoo is picking up the large java script because when I type the domain in and click cached the java script shows up. What can be done? Is my only choice back links? Do I have to build a new home page in .htm format. Any Ideas????