So I designed a simple two-stage test in December to see what would happen. The test is such that if the link passes anchor text in the first stage there is no need to try the second stage.
I embedded an iframed page on one of my older sites. It is well-indexed, has never been penalized, and has sufficient inbound links that I was confident it would be recrawled and re-indexed within a short period of time. It is also a low traffic site (it used to have more traffic a few years ago) so I felt it was probably a safe place to run a link test without attracting too much attention.
The iframed page only contains one in-body HTML element, a link pointing to HighRankings.com with the anchor text of "jill whalen says search engines crawl iframes". This was, until I ran my test, an expression that did not appear in Google's search results (when you wrap quotes around it).
I let the test be through the holidays and checked it today. The expression now appears in Google's search results and it shows only one listing for it:
www.highrankings.com/ - Report spam
by Jill Whalen · in 4,445 Google+ circles · More by Jill Whalen
Over the past 16 years, SEO Consultant, Jill Whalen has worked with hundreds of SEO clients across more than 40 industries to enhance their online presence ...
I don't know how long the link's value will remain in the index, as I will take it down from my site soon. But for now you can use this query to see that Jill's site is indeed ranking for the expression above.
After I publish this discussion, this query will no longer return no results but for now it tells me:
There are rogue crawlers out there which DO crawl iFramed content and republish it on suspicious Websites. That was another reason why I chose the low-traffic site I used for my test. Had I found this anchor text (or the link) on other sites I would have been forced to go to stage two of the test plan to see if I could filter out any influence from rogue crawlers.
I'll say that I am .01% uncertain about any possible contamination of the test from unforeseen factors.
I did, by the way, embed a robots meta directive on my iframed page with "noindex,nofollow,noarchive". This appears to be the only safe way to ensure that iFramed content does not appear in search results. I don't know when that changed but Jill is correct in saying you can no longer rely upon iFramed pages NOT being crawled and indexed (it was always sketchy anyway, as the iFramed pages could have been found through other links).