I am compiling mongodb in an environment where I have multiple includes and library pathes.
I had to modify SConstruct to pass these pathes :

before( SConstruct line 253):

if has_option( "libpath" ):
env["LIBPATH"] = [get_option( "cpath" )]

if has_option( "cpppath" ):
env["CPPPATH"] = [get_option( "cpath" )]

after:

if has_option( "cpppath" ):
for x in GetOption( "cpppath" ).split( ":" ):
env.Append( CPPPATH=[ x ] )

if has_option( "libpath" ):
for x in GetOption( "libpath" ).split( ":" ):
env.Append( LIBPATH=[ x ] )

that's all.
It's compiling now with
scons all \
--cpppath=$(echo $CPPFLAGS|sed -e 's/ -I/:/g;s/-I//') \
--libpath=$(echo $LDFLAGS|sed -e 's/ -L/:/g;s/-L//') \

Glad to contribute
Guy