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The embedded Alfresco based technology in Content Services does have an implementation JCR. You could use its java APIs to program to for storing content in content services.
For connectors to other repositories the thing to use these days is CMIS, a new industry standard. With this, you will be able to connect to content repositories that don't have JCR APIs (SharePoint, others)
http://wiki.alfresco.com/wiki/CMIS
lists server implementations,client apis (chemistry and alfresco also have java client api implementations), client user interfaces
( CMIS Spaces flex/actionscript client apis and client user interface is something I worked on)
Steve
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