Apple has released Java 1.3.1 and 1.4.2 Release 2 which, according to the company’s notes, “delivers improved reliability and compatibility for Java on Mac OS X v10.4. This release includes Java 2 Platform Standard Edition versions 1.3.1_16 and 1.4.2_09.”
The 45.3MB download is available via Mac OS X’s Software Update. More info and standalone installer here.