Custom Alert Template to a specific list

Create a new custom template with a unique Name attribute in your working copy of AlertTemplates.xml (You can copy paste the entire section with Name SPAlertTemplateType.GenericList, change the name and modify the sections you want to). Modify the template as necessary. After restarting IIS, write object model code to set the list alert template
SPAlertTemplateCollection ats = new SPAlertTemplateCollection((SPWebService)(WebApplication.Parent)); //give appropriate values for WebApplication
list.AlertTemplate = ats[“name from above”];
list.Update();


http://blogs.msdn.com/sharepointdeveloperdocs/archive/2007/12/07/customizing-alert-notifications-and-alert-templates-in-windows-sharepoint-services-3-0.aspx