Java conditional compilation: how to prevent code chunks from being compiled?

Nope there isn’t any support for conditional compilation in Java.

The usual plan is to hide the OS specific bits of your app behind an Interface and then detect the OS type at runtime and load the implementation using Class.forName(String).

In your case there no reason why you can’t compile the both OS* (and infact your whole app) using Java 1.6 with -source 1.5 -target 1.5 then in a the factory method for getting hold of OS classes (which would now be an interface) detect that java.awt.Desktop
class is available and load the correct version.

Something like:

 public interface OS {
     void openFile(java.io.File file) throws java.io.IOException;
 }

 public class OSFactory {
     public static OS create(){
         try{
             Class.forName("java.awt.Desktop");
             return new OSJ6();
         }catch(Exception e){
             //fall back
             return new OSJ5();
         }
     }
 }