Drush and multisite config I have a new multisite instance with the Backup &amp; Migrate module installed in /sites/all/modules/

When I run drush the bam-* commands don't show as available commands.

I have site aliases set up and if I run drush @site-alias bam-destinations as a test it does show the available backup destinations.

Is there a more correct way to show the list of available commands for all sites as well as site-specific commands?
Did you try drush @site help?  Simply running drush help will show only the globally-available commands; you must change your working directory to the folder with your settings.php file or use a site alias to select a specific site to see the help for drush commands defined in that site's module.

Sometimes, the Drush command cache can get in your way.  Run drush cc drush to reset it.  Since drush @site bam-destinations is working, this is probably not your issue.

If you are still having trouble after trying these things, also try upgrading to the latest version of Drush (HEAD of master), as some fixes that may be related have been committed post-Drush-5.4.  Also try drush @site help bam-destinations and drush @site bam-destinations --help.  If you're still having trouble, please post a bug report in the Drush issue queue.