I am in the process of developing a flash-based rhythm game featuring music written by other musicians. These musicians have given me a non-exclusive license to use their music in my game, and I would like to know what I should to do protect their music. This includes both legal steps I should take (a copyright warning window at startup, like all those old SNES games?) and any technical steps I should take (protecting the actual music files). Any advice is appreciated, this is sort of a first for me. :]

This is a great question, I would like to hear the answer myself.

The musicians are responsible for protecting their own music. All you can do is acknowledge their ownership of it and that you are using it by permission. Ask them what legal wording they want you to use in your game. Got a contract in which they grant you this permission? The wording should be specified in there.

Songs have copyright protection in the US at the moment they are expressed in a tangible medium. So when the musician writes the notes and lyrics on paper or records the song, they have copyright protection. Humming a tune is not protected under copyright. You don't have to do anything specifically to protect their rights, but it is common practice to list the artist's name and the song's copyright notices in the credits. Be sure you have obtained both synchronization/publishing rights and the rights to use the master recording as songs have two copyrights that need to be cleared.