At a previous job, we wanted binary reproducibility - that is to say, building the same source code again should result in the same binary. The problem was, a lot of programs embed the build or configuration date, and filesystems (e.g. squashfs) have timestamps too.
Rather than patch a million different packages and create problems, we put together an LD_PRELOAD which overrode the result of time(). Eventually we faked the build user and host too.
End result: near perfect reproducibility with no source changes.
I've also used it for reasons similar to the GM Onstar example in the article -- adding an "interposer" library to log what's going on.
I've pulled similar stunts with pydbg on a Windows XP virtual machine -- sniffing the traffic between applications and driver DLLs (even going as far as sticking a logger on the ASPI DLLs). That and the manufacturer's debug info got me enough information to write a new Linux driver for a long-unsupported SCSI device which only ever had Win9x/XP drivers.