checking for libbonobo-2.0 >= 2.0.0... Package libbonobo-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libbonobo-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libbonobo-2.0' found
configure: error: Library requirements (libbonobo-2.0 >= 2.0.0) not met; consider adjusting the PKG_CONFIG_PATH environment variable if your libraries are in a nonstandard prefix so pkg-config can find them.
!!! ERROR: gnome-base/gnome-vfs-2.6.0 failed.
!!! Function econf, Line 365, Exitcode 1
!!! econf failed
Didn't get that. I just emerged gnome and although it took a while to do it's thing, it came out right. Just a small thing where xscreensaver didn't emerge and a mixer plugin likes to screw-up (but that basically fixed itself).
Judging from this, I'd try to emerge libbonobo and restart the gnome emerge.