AVR-Chat

Can anyone here give me any pointers as to how to elegantly manage 
multi-target source/binary structures? We're switching from NGW100 to a 
similar ARM-based board but need to continue building for the NGW, plus 
we do a lot of initial coding/test wholly on PC/linux. We currently have 
one source tree and whenever we want to build for a specific target we 
effectively do: make clean ; make -target. Is there a way to drive 
make/gcc which allows the object files and binaries for different 
targets to be kept alongside each other?
TIA,
Mark