Reports online state that apps that are compiled specifically for 64-bit G5 systems will no longer run after the latest Security Update 2005-007 in installed. Affected programs include many command line applications as well as the 64-bit version of Mathematica 5.2.
That something as obvious as this could be missed suggests that Apple really needs to revamp their software quality assurance program.
Apple has released Security Update 2005-007 Version 1.1 to correct the problem:
Security Update 2005-007 delivers a number of security enhancements and is recommended for all Macintosh users.
Security Update 2005-007 v1.1 replaces Security Update 2005-007 v1.0 for Tiger systems Mac OS X v10.4.2. Users who have already installed v1.0 on Tiger systems should install v1.1.
Security Update 2005-007 v1.1 provides a combined 32- and 64-bit version of LibSystem to replace the 32-bit version that was delivered in v1.0. No other changes have been made in version 1.1.