I’ve just released a new plugin for WordPress multisite setups that require additional control over the format of usernames, the Network Username Restrictions Override plugin. By default, the Network Admin user maintenance screens allow usernames to contain only lowercase letters and numbers.
This plugin relaxes those restrictions, similar to how the Blog Name Restrictions Override plugin does for site names.
It should be especially useful for any setup that uses an external authentication system, such as Shibboleth, which sends usernames that look like email addresses.
Update: I’ve released version 1.1, which adds a small fix for increasing the minimum length of usernames.
Update: I’ve released version 1.2, which supports WordPress 3.4.