That doll is just an inside joke... by IanG

Keep this short and sweet since we're getting blasted with non-stop "the island is Atlantis" and "Richard Alpert is RA!" and the like lately ;)

1. Claires messed up doll is some left over pieces parts from Vincent (stated by a caller on Jay&Jacks podcast). Let's just say Vincent as a dog actually died in the crash, and what we saw on the island was actually Jacob manifesting himself as Vincent in the same way MIB manifests himself as Locke. This means that the dogs body is on the island, just like real Locke's body was as well.
2. It would be easy to see that MIB finds it another funny inside joke of making a baby doll out of the carcass of the same thing Jacob took the form of, just another way for MIB to gloat about killing him.
3. But here's the kicker. If you believe Jacob is actually Aaron (which I don't, but this is rather ironic), the fact that something Jacob took the form of ended up as a baby doll in Claires crib, much like he would have been himself when he was a baby, it adds a further level of "screw you" by MIB to the situation.

That's it, short and sweet. I'm not a subscriber myself of the "Jacob is Aaron" camp, but placing a dead version of Jacob in crazy Claires crib does seem like something MIB would get a chuckle out of.