This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
I have used two Java programs communicating via agents written in LISP. You can write data to a file in one JVM and read the file on another. There are bound to be many more ways.
Using a Unix-specific or LISP connection requires certain dependencies in the platform, so you lose independence.
Question too difficult for "beginning Java". Moving thread.