BuddyPress.org

ACTIVATE PLUGINS FOR ALL BLOGS – First and foremost, one has to read the installation instructions of plugin authors. Some plugins might require uploading to wp-content/mu-plugins folder and some to the regular plugin folder or some plugins require to be uploaded to both mu-plugins and regular plugins folder.

Plugins uploaded to mu-plugins folder (per plugin author instructions) are already activated site-wide and will not be seen in Plugins > Installed unless that’s the way the plugin author set it up. Some mu-plugins do not need further configuration in Site Admin > Options or anywhere else, but some mu-plugins still need additional configurations in Site Admin > Options or somewhere else the plugin author specified.

Plugins uploaded to regular plugins folder may need to be activated sitewide in Plugins > Installed panel or may only be activated for a specific blog AND some plugins made for single WP may not be compatible with WPMU. Some Site Admins use the Plugin Commander plugin to activate a specific plugin sitewide. Even so, in certain cases where such plugin is not WPMU-ready/aware, Site Admin has configure settings of such plugin in each new blog or create a function to do so.

Finally, as DJPaul mentioned above, a better way to check if a plugin for single WP works in WPMU install, is to check out the WPMU forums or WPMU related forums and always check installation instructions of plugin authors.

THEMES ONLY FOR MEMBERS – BuddyPress setting – if you allow the BP members to create blogs and these members purchased a theme for their use only, you could activate the theme for that specific blog via Site Admin > Blogs > Edit link and associate that theme with the specific blog. Only that member will see the premium theme in his/her Appearance > Themes panel.

Site Admin needs to be vigilant about uploading free or premium themes in that there might be obfuscated or encrypted codes within the theme as you don’t exactly know where theme was downloaded from. In addition, some advanced themes would require uploading different theme files in root of installation to wp-admin and/or wp-includes folder which might totally break your install.

Excuse the long post, going thru a lazy rainy afternoon.