Any headphones, no matter the quality, may damage your ears. As the above poster said, look into higher quality headphones; and look into headphones that will seal out outside noise (which can be anything from high-end in-the-canal with custom tips to those earmuff types), but always keep your music at a reasonable volume.
If you listen to I Pod in a noisy area - riding the subway- the loud volume in a closed ear phone situation can cause loss. But normal listening at home shouldn't have a hearing effect.
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The type of head phone that is issued standard with the i-pod is frankly junk, and probably costs around 1 dollar to build the thing. Also because it sits on the out side of the ear, most people raise the volume to compensate for back ground noise... which in turns me you are exposing your self to higher levels of sound pressure.
To best way to combate against back ground noise and decrease sound pressure levels/volume of your i-pod in order to hear your music is through the use of sound isloation head phones.
Google: Shure IEM, Etymotic Research ERP3, Jays, Klipsch, Creative, Ultimate Ears etc. There are a lot of isolation head phone companies out there, and they can range in price and quality. I am actually deeply involved in a company that makes these types of head phones.
That said, IEMs can damge your ears if you turn up you i-pod too much.