I have trouble understanding the gcc compiler provided by OSX 10.6 snow leopard, mainly because of my lack of experience with 64 bits environments.
$ cat >
i686-apple-darwin10.0.0 contains an x86_64 folder which is not understood by most versions of autotools. In other words, I'd say that the gcc compiler is unfortunately nothing short of a joke on Snow Leopard. Why you would bundle 32-bit and 64-bit libraries into i686-apple-darwin10.0.0 is beyond me.
$ ls /usr/lib/gcc
i686-apple-darwin10 powerpc-apple-darwin10
You need to change all your autotools configure files to handle looking in *86-darwin directories and then looking for 64-bit libraries I'd imagine.
As with your system, my mac mini says its i386 even though its obviously using a 64-bit platform, again another mistake since its distributed with 64-bit hardware.
$arch
i386