Why not modify their start scripts (or create them if they don't have them) to call a central server for an update. That way, all you need do is have the users shutdown one night, and the next restart get the script to load the new software.
see
http://www.microsoft.com/technet/prodtechnol/windows2000serv/maintain/optimize/startw2k.mspx

Otherwise you might need something like dameware to individually access the machines, but it still needs to be loaded.