Debugging iframes with Chrome developer tools
In the Developer Tools in Chrome, there is a bar along the top, called the Execution Context Selector (h/t felipe-sabino), just under the Elements, Network, Sources... tabs, that changes depending on the context of the current tab. When in the Console tab there is a dropdown in that bar that allows you to select the frame context in which the Console will operate. Select your frame in this drop down and you will find yourself in the appropriate frame context. :D
Chrome v59
Chrome v33
Chrome v32 & lower
Currently evaluation in the console is performed in the context of the main frame in the page and it adheres to the same cross-origin policy as the main frame itself. This means that you cannot access elements in the iframe unless the main frame can. You can still set breakpoints in and debug your code using Scripts panel though.
Update: This is no longer true. See Metagrapher's answer.
When the iFrame points to your site like this:
<html>
<head>
<script type="text/javascript" src="/jquery.js"></script>
</head>
<body>
<iframe id="my_frame" src="/wherev"></iframe>
</body>
</html>
You can access iFrame DOM through this kind of thing.
var iframeBody = $(window.my_frame.document.getElementsByTagName("body")[0]);
iframeBody.append($("<h1/>").html("Hello world!"));