The best practice approach to this situation is to use Active Directory integration with Operations Manager, and to couple that with a software distribution mechanism (and/or including the OpsMgr agent in the images for new systems). Details on this process are available at: http://ops-mgr.spaces.live.com/blog/cns!3D3B8489FCAA9B51!1034.entry. Pete and Raphael wrote an article about AD Integration for large environment including some LDAP query tips which is available at: http://www.systemcentercentral.com/tabid/144/IndexId/57613/Default.aspx
Powershell can be used to schedule discovery and installation as well (see http://tarek-online.blogspot.com/2007/07/how-to-schedule-discover-and-install.html for details on this).
Additionally there are multiple methods to deploy the Operations Manager agent which are discussed at: http://clintboessen.blogspot.com/2009/05/ways-to-deploy-agents-in-scom.html (or in the Unleashed book on pages 385-403)
SystemCenterCentral has an article about a method that they have used to schedule OpsMgr Discovery and Agent Deployment without AD integration which is available at: http://www.systemcentercentral.com/Details/tabid/147/IndexId/12981/Default.aspx