The best way is to use the new Client Resource Management API in DNN 6.1+.

ClientResourceManager.RegisterScript(BasePage, pathtocss); 

 If you need to support older DNN, you can use something like:

string key = Path.GetFileName(pathtocss);
            if (!BasePage.ClientScript.IsClientScriptBlockRegistered(key))
            {
                BasePage.ClientScript.RegisterClientScriptBlock(typeof(Page), key, "<script type=\"text/javascript\" src='" + GetModulePathWeb(pathtocss) + "'></script>");
            }

Thanks,

Mike