Store them in a databse or in a seperate file? Your question is very vague, maybe I don't understand what you are asking.

A simple form formmail.pl style form with city, state and country fields, the country fields are a drop down and they are being indexed as page content.

How do I not show or excluded the forms variables from being used as content that the search engines index but rather keep them as tools on the page as they are intended?

I don't know that you can if that is the case. The form fields (in some way) have to be in the html source code. Maybe someone will know something or you can ask in a forum that specializes in search engine topics and not cgi/perl. Personally, I can't think of way except to use a robots.txt file and exclude the folder the page is in from being indexed. Of course only friendly search engines will obey the robots.txt file.

perhaps you could obscure the form variable values from search engines by using javascript to valuate the form variable when the page gets loaded.

Well in the past I had link to setup sign up pages but times seem to be dictating the request form on each high end widget page. I have thought of the javascript method, but was just checking to see if anyone has had some better ideas... I may experiment with that or a php insert of some sort. Its needed post haste though... Amazingly negative effect on the keyword totals / duplicate content issues I am suddenly getting back from the big g...