Opening popup window in ASP.NET is quite simple,but you need to very concern about concatenation on javascript and as well as ASP.NET concatenation.
I spent more time on this silly issue,atlast i rectified.
Here i attach my querystring and its value from the selected dropdown list control.
string result = DropDownList1.SelectedValue.ToString();
string script = "";
Page.RegisterStartupScript("myScript", script);