Other than:
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Using royalty free music
Using music specifically permited to be used in such a way (for example I use SonicFire)
Getting expressed written permision
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You are at the whim of what some activist judge decides is FAIR USE. In all reality, provided your distribution stays low, you'll never hear a word from anyone on this issue. I try and use non commercial music now becuase some of my movies have gotten some publicity on major websites, and I just dont need to have to reencode a movie (and re-edit for artistic emphasis) after recieving some crappy cease and desist letter.
While SonicFire is good, its kinda pricey, and for a more real feel...Id encourage you to contact small independant bands. Most would give you permision to use their music for free, cause they'd love the plug in the credits!