I wish all WordPress Plugins had their settings in ONE menu, and all entries in this Plugin Settings menu MUST be named identically to the plugin.
If some of the plugin settings are for administrators, then these should be shown/hidden depending on permissions.
Hide Trackbacks plugin settings must be located at "Plugin Settings" > "Hide Trackbacks"
Currently I've got a plugin running called "Automatic Post Scheduler" (great plugin btw) that adds it's settings to Settings > Write.
Wow, WordPress plugins should not have permissions to add/remove options to the system ones surely?