When adding certificates, stls, ctls and crls to the system I can choose the certificate store.
I have found so far only references to the "my" and "root" stores.
Is there any other?
There are three types of certificate stores in Windows.
Each of the three stores contain a number of folders which certificates go into
These can be seen if you open up an mmc.exe with the Certificates snapin.
Depending on what the certificate is meant to be doing you have to work out where it would go.
Most of the time on the servers we support we use the Computer Account store (as its accessible by all users on a Computer) and put certificates in the Personal store. Some times you might need to add in the signing authority public key certs into the Root and Intermediate Root CAs.
Certificate storeNames are as follows (source) :