Clean Expired Transients is a WordPress plugin (download) that cleans database from every transient older than one minute using safe native WordPress function. It works on multisite too.
By default, it will check for expired transients once daily, though you can call it any time using Clean_Expired_Transients::clean();.
This plugin is a very lightweight, it has no settings, just activate it and it works immediately.
Note that it can be used by developers in their project in any place, it doesn’t require activation and it’s safe to use since it checks is there existing installation, just include it.
Clean Expired Transients is released under the terms of GNU General Public License. It is completely free so if you find it useful you can give something back to author. Your help could be done by giving donation, sending pull request on GitHub, sending bugs and suggestions, promoting plugin in blogs, forums, social networks, and other websites.