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What is so horrible about using cp makefiles/`uname -o`/`uname -m`/Makefile . to copy the correct makefile for the platform?

Not having to maintain multiple Makefiles.

Also multiple incompatible compilers, and cross-compiling… and Darwin doesn't have uname -o, and Linux's uname -o has a / in the output.

Hmm, what isn't wrong with it?

The expression you're looking for is "combinatorical explosion".

You can also have one Makefile that contains conditionals (http://www.gnu.org/software/autoconf/manual/make/Conditional...) based on $(uname -s). I agree with the rant, autoconf has outlived it's purpose.

uname utterly fails when cross compiling.