Yeah let me point you to some resources on this:
http://www.seomoz.org/ugc/new-reality-google-follows-links-in-javascript-4930
Your best resource is from Google here:
To your question though, I do believe Google will execute external javascript files. Ajax stuff I'm not as sure about. They have a primer on this here:
<cite>code.google.com/web/ajaxcrawling/docs/learn-more.html</cite>
The 90% thing I recall from SMX advanced last year I believe. Basically people would try to hide internal links in javascript since using nofollow for pagerank sculpting was debunked by Matt Cutts in 2009. Turned out Google could see most links being created in javascript.
You can read up on that second link there in javascript crawling from Google and it goes into a lot of detail about what they can do, hope it helps.