I am comparing the certificates in my local computer and MMC.exe permits me to view the certificates for “Current User” and “Computer”.
I don’t understand why there would be two “personal” stores. Can someone explain why there are two, and how they interact?
It would be nice to know why those other folders are there too. The only one that I think has a fixed meaning is “Trusted Root Certificates”. The other constant is that Fiddler also seems to put its certificates into “Current User \ Personal”

For example; FedUtil will only use certificates located in the following location (web.config)
<serviceCertificate findValue="6CB9aaaaa636EBF52980152CDCB02D3BBBBBBBBB" storeLocation="LocalMachine" storeName="My" x509FindType="FindByThumbprint" />
It’s mostly a matter of what their intended scope of usage is. The “Local Machine Personal” store contains certificates used either by applications as client/server certificates and belong to this computer only; whereas the “Current User Personal” store contains certificates not bound to any particular machine (for example, you may have a certificate you use to digitally sign documents on several different machines).