Iframes, AJAX, JS, Etc.

[AMHC]

Just started SEO on some legacy sites running JS navigation. Are there any proven ways to stop Google from parsing links and passing internal linkjuice? Ex: iframes, Ajax, JS, etc. Google is parsing some JS links on a couple of our legacy sites. The problem is that some pages are getting link juice and others aren't. It's also unpredictable which links are parsed and which aren't. The choice is rebuild the navigation (ouch), or figure out a way to block JS links entirely and build a simple text based secondary nav for link juice distribution. I definitely don't want to use nofollow.

Any thoughts?