First of all clean the system:

# Clean apt cache:
sudo apt-get clean

# Remove old kernels:
sudo apt-get autoremove --purge

# Then run zerofree, which is specific to dynamic VBoxes
# Based on: https://dantwining.co.uk/2011/07/18/how-to-shrink-a-dynamically-expanding-guest-virtualbox-image/

# Boot to recovery mode then run the below commands.

mount -n -o remount,ro -t ext3 /dev/sda1 /

zerofree -v /dev/sda1

shutdown -h now

# You then need to make a clone of the VBox (since we're not using .vdi format)