This is the secret sauce that makes every implementation unique. Camlistore, IPFS, StrongLink (my project), and others all have different answers. I think the important thing is that they all use hash URIs that can interoperate. Then you can find the content using whichever system you prefer or makes the most sense.

StrongLink doesn't use a distributed hash table, because one of my requirements is that it must work offline. In StrongLink, you pull from other repositories you're interested in, and then always resolve your requests against your own repo (locally).