Gmail strips out any content between
<script> tags before displaying the message. If an e-mail has script tags in it it doesn't mean google will automatically mark it as spam but it could be one of the things that increases the chance.
Most web mail providers and email clients will (or should) do this to prevent against xss (cross-site scripting) attacks. Read more about these here.
in an email and emailing it your gmail account - you won't see any popup dialogs when you open the email.