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Although only applicable to a select few people—2nd Gen iPod Shuffle users who also have the in-ear headphones—this mod is pretty cool. Basically, you stick your iPod Shuffle into the case that comes with the headphones after you cut out the two little pins. That's all. So it's not really a mod so much as an organizational technique.

Now to find a way to make this a bit more Altoid-y.

iPod Shuffle Gen 2 (New One) Travel Case [Instructables via MAKE]