Here's a method that I just wrote today, so that I can pass as many message boxes to the page as I want to:
/// <summary>
/// Shows a basic MessageBox on the passed in page
/// </summary>
/// <param name="page">The Page object to show the message on</param>
/// <param name="message">The message to show</param>
/// <returns></returns>
public static ShowMessageBox(Page page, string message)
{
Type cstype = page.GetType();
// Get a ClientScriptManager reference from the Page class.
ClientScriptManager cs = page.ClientScript;
// Find the first unregistered script number
int ScriptNumber = 0;
bool ScriptRegistered = false;
do
{
ScriptNumber++;
ScriptRegistered = cs.IsStartupScriptRegistered(cstype, "PopupScript" + ScriptNumber);
} while (ScriptRegistered == true);
//Execute the new script number that we found
cs.RegisterStartupScript(cstype, "PopupScript" + ScriptNumber, "alert('" + message + "');", true);
}