If your software should run on both JRE 1.5 and 1.6, then why don't you just develop only 1.5? Is there a reason why you absolutely need to use features available only in Java 6? Are there any third-party libraries that run on Java 1.5 that contain equivalents for the 1.6 functions you want to use?
Maintenance of two basic codes, their synchronization, etc. - This is a lot of work and probably not worth the effort compared to what you get.
Java forcourse does not have a preprocessor, so you cannot (easily) conditionally compile, as you can do in C with preprocessor directives.
, , : , Java 5, Java 6, , , , , Java 5, ( - , , ).