What are the consequences of running a Java class file compiled in JDK 1.4.2 on JRE 1.6 or 1.5?
The Java SE 6 Compatibility page lists the compatibility of Jave SE 6 to Java SE 5.0. Furthermore, there is a link to Incompatibilities in J2SE 5.0 (since 1.4.2) as well. By looking at the two documents, it should be possible to find out whether there are any incomapatibilities of programs written under JDK 1.4.2 and Java SE 6.
In terms of the binary compatibility of the Java class files, the Java SE 6 Compatibility page has the following to say:
Java SE 6 is upwards binary-compatible with J2SE 5.0 except for the incompatibilities listed below. Except for the noted incompatibilities, class files built with version 5.0 compilers will run correctly in JDK 6.
So, in general, as workmad3 noted, Java class files compiled on a older JDK will still be compatible with the newest version. Furthermore, as noted by Desty, any changes to the API are generally deprecated rather than removed.
From the Source Compatibilities section:
Deprecated APIs are interfaces that are supported only for backwards compatibility. The javac compiler generates a warning message whenever one of these is used, unless the -nowarn command-line option is used. It is recommended that programs be modified to eliminate the use of deprecated APIs, although there are no current plans to remove such APIs entirely from the system with the exception of JVMDI and JVMPI.
There is a long listing of performance improvements in the Java SE 6 Performance White Paper.