After being puzzled by this error for some time, I finally was able to solve it with lots of help from my friend Simeon. GTK+ ./configure failed both on emerge gtk+ and on a manual source build with these errors.

configure:33559: gcc -o conftest -g -O2 -Wall -I/usr/include/pango-1.0 -I/usr/include/glib-2.0 -I/usr/lib/glib-2.0/include -I/usr/include/cairo -I/usr/include/freetype2 -I/usr/include/libpng12 -I/usr/include/pixman-1       conftest.c -lpangocairo-1.0 -lpango-1.0 -lcairo -lgobject-2.0 -lgmodule-2.0 -ldl -lglib-2.0    >&5
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderFindStandardFormat'
/opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXrender.so.1: undefined reference to `XMissingExtension'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderQuerySubpixelOrder'
/opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXrender.so.1: undefined reference to `XextRemoveDisplay'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderSetPictureFilter'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderCompositeTrapezoids'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderCompositeText32'
/opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXrender.so.1: undefined reference to `XextFindDisplay'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderCompositeText16'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderCompositeText8'
/opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXrender.so.1: undefined reference to `XextAddDisplay'
/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/../../../libcairo.so: undefined reference to `XRenderSetPictureTransform'
collect2: ld returned 1 exit status
configure:33566: $? = 1

While installing cairo, I got these warnings:

/sbin/ldconfig: /opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXxf86vm.so.1 is not a symbolic link
/sbin/ldconfig: /opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXxf86misc.so.1 is not a symbolic link
/sbin/ldconfig: /opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXxf86dga.so.1 is not a symbolic link
/sbin/ldconfig: /opt/blackdown-jdk-1.4.2.03/jre/lib/i386/libXv.so.1 is not a symbolic link
...

I found this:

grep -R VMHANDLE /etc/
/etc/csh.env:setenv VMHANDLE 'blackdown-jdk-1.4.2'
/etc/env.d/20java:VMHANDLE=blackdown-jdk-1.4.2
/etc/profile.env:export VMHANDLE='blackdown-jdk-1.4.2'
/etc/profile.csh:setenv VMHANDLE 'blackdown-jdk-1.4.2'

Opened up /etc/env.d/20java and commented everything. Then I did:

env-update
source /etc/profile

And I did:

emerge -av cairo gtk+

Which resulted in GTK+ being correctly configured, compiled, linked and installed!

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