I'm trying to clean up my engine's dependencies on third party libraries, and decided to do it TEH TRVE UNIKS way, by actually installing them. Now, I wonder how to convince make to create universal binaries. I tried to just pass
in CFLAGS, but it doesn't seem to take...

Does anyone have a decent methodology for this?

Build it 2-6 times with different settings and lipo the results. This tells you all you need to know ( I hope ): OneSadCookie: Universal Binaries from Autotool'd Projects

For examples of it in action, http://onesadcookie.com/svn/Third-Party

I had to recently build a number of third party libraries from the command-line and found this tech note immensely helpful.

http://developer.apple.com/technotes/tn2005/tn2137.html

Their two approaches both have serious flaws. The first approach doesn't work for projects which care about byte order or type sizes (ie. everything), and their second requires a machine capable of running the code that's being compiled.

Mine (which is a refinement of their second, if you want to look at it that way) requires that the project support cross-compilation (which may not be true for all projects, and for some projects will require additional configure args - ruby is in this basket), but it allows you to build all six (currently-)possible architectures from a single machine.