(For instance, I don’t particularly want people seeing the Domain Mapping plugin but want them to be able to enable Gravity Forms.)
The essential plugin for every multisite install! Manage plugin access permissions across your entire multisite network.
Network activated plugins are hidden from the normal site plugins menu, though they are active regardless.
Plugins installed that are not network activated are visible to individual sites and can be activated on a per-site basis.
I use Exclude Plugins – http://wordpress.org/extend/plugins/exclude-plugins/ – It works.