Software isntalled on a 2000 Pro desktop have a permission scheme identical to the one on servers... i.e. the program has an owner and permissions scheme.
In practice when installing SW on a 2KPro PC you should be the Administrator, if this is not possible you can change the owner later. Also you can set permissions by right clicking on folders, icons, etc. and then using the Security tab to add domain groups, passwords.
To make this manageable you really need to have some sort of a standard. I world recommend "program groups" in your domain that contain users that are allowed to run a certian application anywhere. Then when you install the application, you set this group (and adminstator) as having rights to the program.