How do I have a different set of plug-ins on my main site and on network sites?

I’m setting my my first multisite. How do I set up the site so the primary site has access to one set of plug-ins, and the network sites have access to a different set? There are so many plug-ins (especially from WPMU) that manage multisite issues, but obviously I don’t want these plug-ins showing up on the network sites. Thanks.