Now in Software Update:
Java 2 Standard Edition (J2SE) 5.0 Release 4 delivers improved reliability and compatibility for Java 2 Platform Standard Edition 5.0 on Mac OS X v10.4.5 and later. This release includes J2SE version 1.5.0_06. With this update J2SE 5.0 becomes the preferred Java version, superseding Java 1.4.2.
Additional information can be found in the Apple Knowledge Base.
Java-based applications will run with J2SE 5.0 unless they specifically request Java 1.4.2. To change the default back to version 1.4.2 on a system-wide basis, see the instructions here.