Don't export CFLAGS from your .bash_profile or any other dot file. Your home directory could live on for decades, the system you're currently using is transient.
There's a guide on Apple's web site, Porting UNIX/Linux Applications to Mac OS X, that talks specifically about how to make autoconf
and make
and other similar build systems fit into the Mac OS X Universal Binary scheme. If you're going to build cross-Unix applications on Mac OS X, you need to read and understand this guide.
That said, I strongly question why you want to build Apache 64-bit. Just because Leopard can run 64-bit software doesn't mean you want all software on your system to be 64-bit. (It's not Linux.) In fact, virtually none of the software that ships with Leopard runs 64-bit by default, and most of the applications included with Leopard only ship 32-bit.
Unless you have a pressing need to run Apache 64-bit, I wouldn't bother trying to build it that way.