You can find a much more comprehensive Makefile that will work with regular sketches and libraries here:
http://code.google.com/p/arducopter/source/browse/trunk/libraries/AP_Common/Arduino.mk
It includes some fairly hairy awk that is quite faithful to the processing that Arduino performs on sketches; you can break it but not easily.
The ArdupilotMega/ArducopterMega project uses this as part of their automated build testing, and it's also suitable for calling from Eclipse (why I built it in the first place).
= Mike