codice:
<%@ Page Language="C#" %>

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<script runat="server">

	protected void button1_Click(object sender, EventArgs e)
	{
		this.RegisterStartupScript("popup", "<script" + ">"
			+ "window.open('','popup','width=300px,height=300px');"
			+ "</scrip" + "t>");
	}
</script>

<html xmlns="http://www.w3.org/1999/xhtml" >
<head runat="server">
    <title>Untitled Page</title>
</head>
<body>
    <form id="form1" runat="server">
    <div>
		<asp:Button ID="button1" runat="server" Text="Button" OnClick="button1_Click" />
    </div>
    </form>
</body>
</html>
non funziona, nè con Firefox, nè con IE

almeno che tu non abbia sbloccato il blocco popup