One factor that people have trouble with when it comes to their squat depth is not having enough ankle mobility (primarily ankle dorsiflexion).
One thing that can be limiting this is the strength/flexibility of your soleus. The soleus is a calf muscle which originates just below the back of our knee, travels down the back of the shin bone and attaches inserts into the achilles. Soleus is more active during the squat position due to the bent knee nature of the squat.
The following exercises focus on improving your soleus strength and mobility by improving your control of the soleus in a lengthened position as you squat down, thus improving your squat depth!