Where is the system wide PATH shell variable set in OS X?
On a shell level, the PATH variable is set in /etc/profile by calling /usr/libexec/path_helper. To add your own paths, you can add files with a path in it to /etc/paths.d/:

pse@Fourecks:~$ ll /etc/paths.d
total 8
-rw-r--r--  1 root  wheel  13 Jul 22 07:02 50-X11
-rw-r--r--  1 root  wheel  12 Aug 13 14:12 TeX
pse@Fourecks:~$ cat /etc/paths.d/TeX 
/Library/TeX/texbin


That's the safer way than editing /etc/profile, /etc/paths or any other system-provided file which may get overwritten with the next OSX upgrade.