i have created a mich simpler Makefile to compile the example from the SDK. This one is prepared for the AT firmware. Shouldn't be too hard to figure out what to modify to use it for the IoT firmware as well. Small README included.
NOTE: Updated Makefiles are at http://www.esp8266.com/viewtopic.php?f=9&t=142&start=20#p772
And here is a tool that will create the proper firmware files from the compiled object file. The original SDK uses that gen_misc.bat thing, which is just silly. That thing calls objcopy and objdump repeatedly, the starts a python script which in turn starts an exe file to create the files. My tool will do all that in one quick go. The above Makefile makes use of this tool already. A precompiles .EXE for Windows is included, as well as a README and the full sources (it's licensed under the GPL v2).
NOTE: There was a bug in the esptool i posted. It is fixed, and can now be found at http://www.esp8266.com/viewtopic.php?f=9&t=142&start=20#p772