I am encountering a similar error when trying to compile from the 0.6.2 source on my iBook.  I tried pulling the various frameworks from the 0.6.2 .app (installed from a .dmg) into /Library/Frameworks and have ensured that I've got the latest version of Xcode from ADC.  The results are as follows:

$ ./build.sh uqm
'echo -n' capable echo found.
Sed stream editor found.
tr found.
Make found.
build/unix/build.sh: line 1: libmikmod-config: command not found
build/unix/build.sh: line 1: libmikmod-config: command not found
build/unix/build.sh: line 1: libmikmod-config: command not found
GNU C compiler found.
We have a C preprocessor.
We have a C dependency generator.
We have a C compiler.
We have a linker.
We have a Objective-C preprocessor.
We have a Objective-C dependency generator.
We have a Objective-C compiler.
Rez resource compiler (Apple Developer Tools) found.
We have a MacOS X resource compiler (Rez).
Little-endian machine detected.
Simple DirectMedia Layer not found.

Full disclosure: this is the first time I've done anything substantially more complicated than Hello World! in around, oh, a decade.  I'm also more than a little tired now.  It's highly likely I'm doing something obvious wrong - any ideas?

Perhaps I shouldn't be doing this after the week I've had...   

Quick update - installing libmikmod again via Fink took care of those errors.  I also attempted to update SDL, with no luck.