Ive just been trying to build Mapnik on my stock Debian Etch box. Mapniks build system couldnt find the required Boost libraries on its own, and it wasnt possible to just tell it where they were
Read about the troubles here
Scons seems to be an immature tool, that simply doesnt solve half the problems that Autoconf does. Its probably easy to use, but why bother if it doesnt deliver the goods either. Its pretty easy to write a plain makefile that compiles the code on your chosen OS. If you cant be bothered to go through the pain of making it cross platform (and I dont blame you), then dont use something half-arsed like Scons – that just makes everyones life harder.