PHPCR is an attempt to port the Java Content Repository (defined by Java Interfaces) to PHP. The port is done in the spirit and not to the letter. PHPCR has "phpized" the API to make it more usable in PHP. See JCR to PHPCR in code documentation for a full list what is different.
What is the relation between JCR and CMIS?
They are handling similar issues on different levels, and are therefore mostly complementary. JCR is an API, while CMIS is a protocol for SOAP and Atom. JCR has the notion of trees built in.