A lot of people swear by breaking in their headphones- I'm half certain my current pair sounds as good as it does by duty as a speaker. It isn't going to make an aweful pair sound better, but it might make a good pair sound better, or help an excellent pair of headphones reach their full potential.
Of course, some of you might consider it snake oil, or find that it dosen't help. Your milage would vary. This setup might work for muffling other things i suppose
The method i prefer is to plug in the headphones to a mp3 player, and just play random stuff at maximum volume for a few hours, let it rest and do it again, a few times. Your milage may vary, and some people use pink noise at lower than normal volumes. Your milage may vary.
The instructable below covers a setup that's cheap, made out of things you'd have around the house (you arn't going to break in headphones everyday) and mutes the headphones so you can break them in without disturbing anyone, or ruining your hearing.
2 pillows or more.
1 plastic storage box, preferably close to same size at the base as the pillows
1 sound source, preferably nothing powerful enough to blow out the headphones, but loud enough to give em a workout. A MP3 player of some sort would be good for this