I'm really starting to suspect hardware as well based on your comments here and elsewhere compared to others experiences. Or something really odd that you are doing based on your symbolic links comment.
I do remember getting really strange issues with my old Powerbook when the IDE controller was going out. It was very hard to detect, and a replacement mainboard fixed it. Initially, under certain load, the drive would get remounted read only due to errors detected. The hard drive was replaced, and the system was checked for errors for a while and came up clean. I took the system back, and began having similar issues again.
In the end, the combination of trying to install World of Warcraft off disc, along with being plugged in, and energy saver set to highest performance would reproduce the problem every time. Nothing else, including diagnostic programs found a problem. Something about the high CPU usage along with heavy IO induced the issue. WoW install discs use quite a bit of compression, so the CPU was busy during install.
It's possible your problems started with Leopard doe to a similar issue. Leopard does generally use more CPU time then Tiger with the additional thing added into the OS, and maybe it was enough to trigger the problem.
For the record, this is ny /bin on a 10.5.4 install on an Intel mac:
-r-xr-xr-x 1 root wheel 46720 Nov 28 2007 [
-rwxr-xr-x 1 root wheel 1244928 Mar 4 2008 bash
-r-xr-xr-x 1 root wheel 43296 Mar 5 2008 cat
-r-xr-xr-x 1 root wheel 56720 Apr 20 13:32 chmod
-r-xr-xr-x 1 root wheel 56208 Apr 20 13:32 cp
-rwxr-xr-x 1 root wheel 610864 Sep 23 2007 csh
-r-xr-xr-x 1 root wheel 56096 Nov 28 2007 date
-r-xr-xr-x 1 root wheel 59776 Apr 20 13:32 dd
-r-xr-xr-x 1 root wheel 51424 Apr 20 13:32 df
-r-xr-xr-x 1 root wheel 38336 Nov 28 2007 domainname
-r-xr-xr-x 1 root wheel 38320 Nov 28 2007 echo
-r-xr-xr-x 1 root wheel 114000 Mar 5 2008 ed
-r-xr-xr-x 1 root wheel 46944 Nov 28 2007 expr
-r-xr-xr-x 1 root wheel 38416 Nov 28 2007 hostname
-r-xr-xr-x 1 root wheel 38640 Nov 28 2007 kill
-r-xr-xr-x 1 root wheel 2103664 Sep 24 2007 ksh
-rwxr-xr-x 1 root wheel 133312 Apr 3 19:48 launchctl
-r-xr-xr-x 1 root wheel 38752 Apr 20 13:33 link
-r-xr-xr-x 1 root wheel 38752 Apr 20 13:33 ln
-r-xr-xr-x 1 root wheel 73696 Apr 20 13:33 ls
-r-xr-xr-x 1 root wheel 38640 Apr 20 13:33 mkdir
-r-xr-xr-x 1 root wheel 47696 Apr 20 13:33 mv
-r-xr-xr-x 1 root wheel 218640 Apr 20 13:33 pax
-rwsr-xr-x 1 root wheel 85536 Mar 4 2008 ps
-r-xr-xr-x 1 root wheel 38400 Nov 28 2007 pwd
-r-sr-xr-x 1 root wheel 56208 Nov 28 2007 rcp
-r-xr-xr-x 1 root wheel 47616 Apr 20 13:34 rm
-r-xr-xr-x 1 root wheel 38352 Apr 20 13:34 rmdir
-r-xr-xr-x 1 root wheel 1244960 Mar 4 2008 sh
-r-xr-xr-x 1 root wheel 38464 Nov 28 2007 sleep
-r-xr-xr-x 1 root wheel 55744 Sep 23 2007 stty
-r-xr-xr-x 1 root wheel 38128 Dec 10 2007 sync
-rwxr-xr-x 1 root wheel 610864 Sep 23 2007 tcsh
-r-xr-xr-x 1 root wheel 46720 Nov 28 2007 test
-r-xr-xr-x 1 root wheel 47616 Apr 20 13:34 unlink
-rwxr-xr-x 1 root wheel 38544 Nov 20 2007 wait4path
-rwxr-xr-x 1 root wheel 982000 Sep 23 2007 zsh
-rwxr-xr-x 1 root wheel 982000 Sep 23 2007 zsh-4.3.4