I have found window alerts to be very good for getting people to take surveys, sign up for newsletters, or some other productive action. I don't think people are as bothered by them as pop ups but does it have a negative effect on SERPs? Here's an example: http://www.salarymap.com/salary-survey-comparison/salary-list-2.cfm (Note: this alert will show once after a 5 second delay and will leave 5 year cookie so it won't bother you again). Please provide an informed answer like some statement form Google or some data you have gathered. Please don't reply with "umm, I think so"
They (Google Adwords) stopped me from serving up a pop up newsletter sign up forms. They said it disabled the back button (well at least you can't use backspace or alt-left). So they are Javascript aware on the Adwords side and I expect they may penalize on the search engine side.