qgis configure script requires geos-2.x.x and doesn't work with geos-3.0.0-rc1 which was just put in portage tree.
checking for gdal-config... /usr/bin/gdal-config
checking for OGR in GDAL... yes
checking GDAL_CFLAGS... -I/usr/include
checking GDAL_LDADD... -L/usr/lib -lgdal
checking for geos-config... /usr/bin/geos-config
configure: error: Geos Version 2.x.x is needed, but you have 3.0.0rc1!
Ah, sorry, there's nothing like qgis in portage tree, it's my local ebuild. It's several month I touched that so I forgot.
See Bug 56262 if you'd like to help out. ;)