Recently McMyAdmin (MMA) released a version which exports it's group permissions to the bukkit plugin GroupManager.

To enable this functionality,

1. Log into your McMyAdmin panel.
2. Go into the Preferences tab.
3. Click on the Server Features link on the left.
4. Set Permissions Integration to GroupManager.

McMyAdmin will now overwrite GroupManager's existing permissions and you'll need to setup your permissions using MMA's panel. This includes adding your plugin's permission ID's to the groups.

For example, if you're using Essentials, you'll want to add essentials.help to your Everybody group so that everyone use the /help command. You can't just add /help to a group.

Here's Essentials' commands and permission IDs.

For other plugins, check it's plugin page on Bukkit's Plugin Releases forum. Do a Ctrl+F and search for permissions on your plugin's page.