Well this is an interesting question I have, I have installed some plugins now and all is going good, users have access to their plugins menu to activate/deactivate the plugins.
The problem is howerver that some plugins I just want enabled when they create their blog and not listed on that page unless one of the site admins (such as me) view it but no the user.
One example of one of these plugins they should not be able to control is Swith Blog URL, where currently they have to go and actiavte the plugin, then goto the menu to change their URL, I'd much prefer to always have it activated without them having a say in the matter so they just goto the feature in the dashboard and change their blog URL.
However, some such as Akismet I don't mind them having the option of deactiating it or changing the option. I plan of introducing others that some users may decide they don't want as well.
EDIT: Or better yet, is their a way to code the activation and deactivation of plugins in my own script, remove the plugins menu and sub in my own plugin script that:
a) only shows the plugins I want them to control
b) for certain plugins intergrate with paypal to offer it as a paid upgrade