Can I use drush to compare the running modules on two sites on the same server?
I don't know if there is a direct way, but this should work with bash or a similar shell. No idea about how to do that with Windows :) Please comment and I'll integrate it into the answer.

First, save the enabled modules of both sites into a textfield with this command:

drush pm-list --status=enabled &gt; enabled_modules_site_x.txt


Then, you can easily compare the output of these two files with diff.

diff first_file second_file