What are the best practices for connecting SAP and Java?

Can you give complete details on how I can get connected from SAP ABAP to Java? What's the configuration from the Basis point of view, and how do I call from ABAP to Java?

There is not much to say. The connection between SAP and Java is done via RFC or HTTP. For RFC there is the Java Connector, a set of Java libraries that allow you to write your own RFC server in Java that you can call from R/3. The same JCo also builds an API for making RFC calls from Java to R/3.