I do find that the earphone foams start to flatten after a while. Every now and then I replace them and everything has extra bass for a while
I guess wax and dirt flatten them because I tried washing them in soapy water once and they puffed up again.
Some people on another forum were saying they make cuts in the foam where the holes and meshes in the earpods are to allow all the sound through. I did that with mine but it makes them look very untidy and the risk of ripping increases.
Check out what this guy did:
http://www.head-fi.org/t/741422/apple-earpods-are-excellent#post_11028014
foam covers on top of earskinz. Sounds like a good idea for someone who wants that style of earphone.