Export pkg config library path and move into source code directory
http://thebugfreeblog.blogspot.co.uk/2013/03/bring-up-qt-501-on-raspberry-pi-with.html
export PKG_CONFIG_PATH=/home/parallels/rpi/mntrpi/usr/lib/arm-linux-gnueabihf/pkgconfig
export PKG_CONFIG_LIBDIR=/home/parallels/rpi/mntrpi/usr/lib/pkgconfig:/home/parallels/rpi/mntrpi/usr/lib/arm-linux-gnueabihf/pkgconfig
export PKG_CONFIG_SYSROOT_DIR=/home/parallels/rpi/mntrpi
cd /home/parallels/Qt/src/qt-everywhere-opensource-src-5.5.1

ALWAYS MAKE SURE THAT YOU ARE USING A CLEAN DIRECTORY THAT HAS NOT BEEN USED TO BUILD BEFORE

Configure
./configure \
    -opensource \
    -confirm-license \
    -release \
    -opengl es2 \
    -optimized-qmake \
    -no-pch \
    -make libs \
    -make tools \
    -reduce-exports \
    -sysroot /home/parallels/rpi/mntrpi \
    -device linux-rasp-pi-g++ \
    -device-option CROSS_COMPILE=/home/parallels/rpi/tools/arm-bcm2708/gcc-linaro-arm-linux-gnueabihf-raspbian-x64/bin/arm-linux-gnueabihf- \
    -prefix /usr/local/Qt-5.5.1-raspberry
OR
./configure \
    -commercial \
    -confirm-license \
    -release \
    -static \
    -opengl es2 \
    -optimized-qmake \
    -no-pch \
    -make libs \
    -make tools \
    -reduce-exports \
    -sysroot /home/parallels/rpi/mntrpi \
    -device linux-rasp-pi-g++ \
    -device-option CROSS_COMPILE=/home/parallels/rpi/tools/arm-bcm2708/gcc-linaro-arm-linux-gnueabihf-raspbian-x64/bin/arm-linux-gnueabihf- \
    -prefix /usr/local/Qt-5.6.0-raspberry

Edit as per https://forum.qt.io/topic/62264/failed-to-cross-compile-qt-5-6-on-rpi-2-fatal-error-bcm_host-h-no-such-file-or-directory/2
nano qtbase/mkspecs/devices/linux-rasp-pi-g++/qmake.conf
INCLUDEPATH  += $$[QT_SYSROOT]/opt/vc/include
INCLUDEPATH  += $$[QT_SYSROOT]/opt/vc/include/interface/vcos
INCLUDEPATH  += $$[QT_SYSROOT]/opt/vc/include/interface/vcos/pthreads
INCLUDEPATH  += $$[QT_SYSROOT]/opt/vc/include/interface/vmcs_host/linux

Install Qt to RPi
(This will build all modules)
sudo make -j4 install