Using my python.org install:
robin-mbp:~ robince$ which python-config
/Library/Frameworks/Python.framework/Versions/2.5/bin/python-config
robin-mbp:~ robince$ python-config --ldflags
-L/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/config
-ldl -lpython2.5

But if I build a C file with python embedded, the above linker flags
result it in it embedding the system python. Obviously the -lpython2.5
is picking up the system one in preference to the one on the -L path.

From Ronald Oussoren on pythonmac-sig:

The easiest workaround is to open a terminal window and execute the 
following commands:

  cd 
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/config
  ln -s libpython2.5.a libpython2.5.dylib

This will ensure that the OSX linker knows that libpython is a shared 
library and links to this library. By default the OSX linker searches 
for a .dylib on the entire linker path and only then looks for .a files.

Fixed in r77033 (trunk), r77034 (2.6), r77035 (py3k), r77036 (3.1)

Development on the 2.5 tree is closed, I will therefore not backport to 
2.5.

As a workaround you can add -Wl,-search_paths_first to the linker flags to 
ensure that the libpython.a in the framework gets picked up before 
/usr/lib/libpython2.5.dylib.