One of those packages seemingly overwrote the library that James mentioned:

walter at freshinstall:~$ ls -l /lib/libld.so.4
-rwxr-xr-x 1 root bin 530916 2008-04-26 18:43 /lib/libld.so.4
walter at broken:~$ ls -l /lib/libld.so.4
-rwxr-xr-x 1 root bin 583168 2008-08-07 17:04 /lib/libld.so.4

I installed the VirtualBox guest additions, the library file was unchanged, and 
the compiler still worked. Here are the punchin packages I will install:

walter at freshinstall:~$ ls -l *.pkg
-rw-r--r-- 1 walter staff  67584 2008-08-08 11:37 ITpunchin.1.2.1.pkg
-rw-r--r-- 1 walter staff 544256 2008-08-08 11:37 SUNW0punchin-i386.2.2.1.pkg

I installed SUNW0punchin-i386.2.2.1 and everything still worked. Then I 
installed  ITpunchin.1.2.1 and everything still worked! I ran punchctl and 
created an initial configuration and self-signed certificate, and still the 
library file is unchanged and the compiler works.

I don't want to take the next step and register the new certificate since that 
would invalidate my old certificate and break my VPN connection for an hour or 
so. But I'm left with two possibilities, 1) that running punchin breaks the 
library, or 2) that the problem is the order in which packages are added. On my 
first (now broken) machine, I first installed guest additions and punchin, and 
then installed the compiler. On my second (still working) machine I first 
installed the compiler, and then guest additions and punchin.
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