IBM Rational ClearCase

Has anyone used the ClearCase Java API, and how does it compare to the Perl API?

I am not aware of dedicated Perl API. There are some Perl Modules that wrap the ClearTool commands and make them available for use with Perl.

There is a common API for ClearCase called, ClearCase Automation Library or CAL. This is available for a variety of programming languages, but as of 7.0.0 this was replaced with just the Java version of the CAL.

So, depending on your use case you may be able to just use the Perl modules to accomplish your task or you will have to use a the Java version of the CAL to get it done.