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I thought of one way of doing this would be to use an external JS file, but the problem is that search engine can still read the JS file even if you disallowed it from robots.txt. A while ago there was a thread about this that Google was reading external JS files, even if there was a robots.txt file dissalowing it.
I was thinking maybe if there was a way to put code in .htaccess file, that might work. Can .htaccess file be used to launch pop up pages?
Search engine spiders may look at javascript (as text) to find "obvious" urls they might try, but AFAIK they don't programatically parse javascript - the danger of malicious code and all that.