Recent versions of blender depend on app-doc/doxygen[-nodot] (if USE=apidoc). Recent versions of doxygen have a dot USE flag, not a nodot USE flag. Please change the dependency to something like "|| ( <app-doc/doxygen-1.7.6.1[-nodot] >=app-doc/doxygen-1.7.6.1[dot] )" so blender[apidoc] and >=doxygen-1.7.6.1 can be installed on the same system.
Sorry for that, I was reckless + 23 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> blender-2.57-r1.ebuild, + blender-2.60a.ebuild: + Fix dependency on app-doc/doxygen wrt converting useflags 'nodot' to 'dot'. + Fixes bug 405445 by Marien Zwart <marienz@gentoo.org>