mysite.com has an iframe which loads some differentsite.com.
need to run javascript on this loaded iframe document.
Single Or
You could try window.postMessage(message, origin) (it would be parent.postMessage from the iframe and iframeElement.contentWindow.postMessage from the top page) for all of the latest major browsers (Firefox, IE, Safari, Chrome, etc.) and changing/polling window.name for old browsers.
The first question would be, do you have control over the secondary domains, or are you able to persuade the webmasters of these to add additional components?
If so you could easily use easyXDM to call methods across the domain boundry. Demos of this can be viewed here