Pop-up window and SEO

Our company uses pop-up form (which is produced by javascript/AJAX and not by opening a new browser window). The purpose of the pop-up is to invite users to subscribe to our email list. So far, we've found this technique to be an effective way to get more sign ups. The negative impact based on bounce rate, time on site, and other metrics also appear minimal.

However, we are concerned about the impact of using javascript-based popup window on our search engines ranking. We did some research on the web -- with the exception of Matt Cutts' video saying that Google doesn't penalize sites for using pop-up -- there is no evident to suggest that pop-up is bad for ranking or otherwise.

If you know the answer to this question and can point to the source, I'd appreciate it.
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There isn't any penalties that I am aware of, and I watch the space very carefully.

From a user perspective a good implementation has a delay, and also has a link to set a cookie so it doesn't display again.

Alternatively a cookie can be set each time someone follows a link from an email to refresh deleted cookies.

It is also worth experiementing a bit with the bottom of the page slide ups.

Fast load time is important - if you use graphics in the popup then it is good to get them stored on a CDN, or delay the popup long enough to ensure all elements are prefetched.

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It has no effect on rankings.
Why are you concerned about something that
1. You can find no reason why you should be concerned and
2. You've actually found a video from a Google engineer telling you that there is no reason to be concerned
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