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 >
The default compiler on Snow Leopard is gcc4.2, and its default architecture is x86_64. The typical way to build Mac software is to build multiple architectures in separate passes, then use lipo to combine the results. (lipo only compiles single-arch files into a multiple-arch file, or strips archs out of a multi-arch file. It has no utility on single-arch files, as you discovered.)
The bitness of the compiler has nothing to do with anything. You can build 32-bit binaries with a 64-bit compiler, and vice versa. (What you think is the "target" of the compiler is actually its executable, which is different.)
The bitness of the kernel has nothing to do with anything. You can build and run 64-bit binaries when booted on a 32-bit kernel, and vice versa.
What matters is when you link, whether you have the appropriate architectures for linking. You can't link 32-bit builds against 64-bit binaries or vice versa. So the important thing is to see what the architectures of your link libraries are, make sure they're coherent, then build your binary of the same architecture so you can link against the libraries you have.
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
Apple toolchains support multiple architectures. If you want to create a fat binary that contains x86 and x86_64 code, then you have to pass the parameters -arch i386 -arch x86_64
to gcc. The compiler will compile your code twice for both platforms in one go.
Adding -arch i386 -arch x86_64
to CFLAGS may allow you to compile gmp, mpfr, and whatnot for multiple archs in one go. Building libusb that way worked for me.
The real question is... how did you get a 32-bit version of OSX? I wasn't aware that Snow Leopard had a 32-bit version, as all of Apple's Intel chips are Core 2 or Xeon, which support the x86_64 architecture.
Oh, and Snow Leopard only works on Intel chips.
Edit: Apparently Snow Leopard starts in 32-bit mode.