list modules in use in multi-site install (API support?)

Since the modules might vary from site to site in a multisite install, it seems to me you'd have to hit each site's database. From the BASH Programming - Introduction HOW-TO:

        #!/bin/bash
        for i in $( ls ); do
            echo item: $i
        done

So do an ls in your sites directory and instead of echoing them, run the drush module status command with the site passed as an argument for each one.

Looking through the multisite_api (specifically function multisite_api_site_list), which the multisite_maintenance module relies upon, it seems all it does is find a listing of all sites (or more accurately settings.php files), so that doesn't seem to be any faster than the above. Feel free to re-open if you think otherwise since I don't consider myself to be the ultimate authority on this. I just don't think you'll be ale to get around having to parse the database authentication info in each site's settings.php, which drush does, and then hitting the modules in each site's database sequentially.

Yes, you can call drush from within your modules, Aegir does this a lot. See also #349923: drush_invoke : a flexible API for hooking into any and all drush calls..

Alas, there is no reliable way for drupal to introspect and find all these base urls. Most sites use an implicit base url based on the incoming domain of the request. So admin will need to maintain a list of base urls in .drushrc.php file. Once we have that, we could support a --multisite param for any drush command. when that is present, it would iterate over the list and run the same command for all sites. i guess it would accumulate the output from each and show you a nice table at the end. i'd love adrian and owen's opinion on this idea.

Drupal Contrib API to start and then follow some aegir examples, that's all I know of.

Interesting. I'm pretty sure that this requires explicitly stating a base_url in settings.php which is unusual and a bit inconvenient. Maybe we could do our best guess thing based on directory name.

It's always been in the back of my mind to integrate Multisite API with Drush.

Moshe you are correct about $base_url, if $base_url is not explicitly defined, then the directory name may or may not be the $base_url. It won't be if the site:
- uses the default sites directory
- is on a special port
- is in a subdirectory of the domain, or
- the directory name is only a partial match to the $base_url (ex. foo.bar.example.com => sites/example.com/)

Currently Multisite API only returns $base_url if it is explicitly defined. In the documentation I describe this reverse engineering problem. What we could do is have Multisite API return an additional variable, $base_url_derived or the like which would be our "best guess".

I have a long flight on Monday, I might be able to take a closer look at this then.

$_SERVER['SERVER_NAME'] is set by Drush, so depending on that is circular logic...

The $base_url reverse engineering problem is still an issue, but some of the problems touched on in this issue are addressed by site aliases and #628996: Concurrently execute a single drush command on multiple sites.

I think we can discuss more at #628996: Concurrently execute a single drush command on multiple sites. Or reopen this with some clarification about how this issue is different.