Here are some of the things I did to make Kali Linux 2016.1 suit my taste, mostly intended as a note to myself, but posted here in case it helps anyone else.

General checklist

Install aptitude and update everything
Add settings icon to left panel
Enable mouse tap to click in “Settings => Mouse & Touchpad”
Tweaks => Power => Don’t suspend on lid close
Enable sound, but disable alert sound (sonar)
Disable all power saving (“Power”)
Enable privacy settings, purge stuff after 7 days (“Privacy”)
Tweaks => Extensions => Disable Easyscreencast
Settings => Keyboard => Input Sources => Remove superfluous keyboard layouts

Install fun stuff

apt-get -y install \
dconf-editor \
gnome-power-manager \
autossh \
vim \
screen \
iotop \
iftop \
virtualbox \
torbrowser-launcher \
aptitude

Automatically log in as root

Edit /etc/gdm3/daemon.conf

AutomaticLoginEnable = true
AutomaticLogin = root

Enable smartmontools

Edit /etc/default/smartmontools

start_smartd=yes

Shut down with power button

Note: shutdown option missing as of 2016-05-16

gsettings range org.gnome.settings-daemon.plugins.power power-button-action
gsettings set org.gnome.settings-daemon.plugins.power power-button-action 'shutdown'

Encrypted swap

For separate partitions, use the existing guide for Debian.
For swap files in encrypted filesystems, do this:

dd if=/dev/zero of=/.swap bs=1G count=16
chmod 600 /.swap
mkswap /.swap
swapon /.swap
echo "/.swap none swap sw 0 0" >>/etc/fstab

Disable auto-locking and that stupid slide screen

gsettings set org.gnome.desktop.session idle-delay 0

Install qemu and virt-manager

apt-get -y install qemu-kvm virt-manager
systemctl enable libvirtd.service

Set a custom default window manager (like xfce)

I now use the default environment, but it’s here in case anyone finds it interesting anyway

apt-cache search kali-desktop
apt-get -y install kali-desktop-xfce
update-alternatives --config x-window-manager
update-alternatives --config x-session-manager

My tweaks to Kali Linux (note to self)