One of two things happened:
1. Your boy downloaded said stuff.
2. In the process of downloading Limewire, configuring it, or possibly through a .exe file downloaded over the P2P network, you got pwn3d.
Limewire (in and of itself) does not allow other people to store stuff on your computer unless you download those files yourself, at least it didn't when I checked it out a year ago. If it's case #1, you need to deal with your kid, pronto. If it's case #2, a flattening of your (probably still zombied) box needs to be done pronto.