Updated the toolchain to GCC 6.3.0, see first post.
ATTENTION! For compiling older C++ code you may require adding -std=c++98 or -std=gnu++98 compile flag, since GCC 6.3.0 has -std=gnu++14 by default. Also, some warnings are treated like errors, so code fixing is obligatory.
EDIT: So far only fceu320OD (fceux) fails to compile with GCC 6.3.0 because of multiple linking errors. It's recommended to use 4.8.1, 4.9.1 or 4.9.3 in this case.