It is possible to build an iPhone application manually, without using xcodebuild nor an Xcode project?
The idea is to build the application using SCons without creating an Xcode project. I know there is the codesign command line tool, that I could use, but before I start reverse engineering the Xcode build process, I was wondering if anybody has experience with this or has done it before.
Yes, It's possible to write a makefile using gcc. You're going to want to set your GCC to use frameworks from /Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS3.1.2.sdk/ (frameworks being in system/library/frameworks, and usr/lib).
As far as specifics, I think you're going to have to work that out yourself - but pay careful consideration to the architecture options in GCC and you should have something working quickly.