I did a quick test with google's "Note In Reader" bookmarklet in IE8. The first time I clicked it I got an error about a pop-up being blocked. I clicked to allow the pop-up (which caused the page to refresh) and then it seems to have worked. It brought up a pop-up window which let me add a comment on the page I was on. It's definitely functional, but not ideal.
Hmm, I wonder how they did that. Maybe the popup has different permissions than the iframe, or maybe they pass the selected text. Unfortunately, their code is obfuscated, but thanks for the tip.