Question: I'd like to know if I can develop my program with the current JRE 7u45 and later run it on an AS400 with IBM J9 VM build 2.4, JRE 1.6.0.
Or will I have to use the 1.6.0 JRE to develop my program? As long as I don't use commands that were introduced later the program should work, shouldn't it?

Answer: 
I do this daily.

The best way to be absolutely certain that the code will work as written without accidentally using features not present is to use java 6 for development. For eclipse that is installing a java 6 JDK and adding it to the Eclipse JRE preferences. 

Note that the built in File support does not support CCSID's. Use IFSFile in jt400.jar instead.

Also, if you use JAVA or RUNJVA to invoke your program, you can use SystemDefaults.properties to provide system properties and JVM arguments. Check infocenter.
While you compile the program you need to use the "-target" flag and set it to 1.6