Cisco calls Savitar Two-Face in relation to half his face being scarred. This is a reference to the famed Batman villian Harvey Dent.
Cisco says to reverse the polarity of the neutron flow. Reversing the polarity (but without the neutron flow) is often mentioned as a parody for solving all problems by just reversing the polarity of something, which originated with the Third Doctor in Doctor Who. This way to solve problems was spoofed in Stargate SG-1 the 200 episode when the team spoofed Star Trek TOS as well. So this line pays homage to many sci-fi shows.
Written on H.R. Wells' grave "The two most important days in your life are the day you are born and the day you find out why - Mark Twain"