Cisco wears a rock, paper, scissors, lizard, Spock shirt towards the end when they take care of Dr. Wells. This is a nod to Dr. Sheldon Cooper on The Big Bang Theory, who often wears The Flash t-shirts, daydreams of being The Flash and dresses as him for Halloween.
Eobard Thawne is a comic book character known as the Reverse-Flash (aka Professor Zoom) who made his comic debut in Flash #139 (Sept. 1963). Thawne was from the future and idolized The Flash. After recovering one of his suits in a time capsule, Thawne gained Barry's powers. He went back in time to meet him but learned that he himself would become a villain, thereby losing his mind and actually becoming a villain.
In the DC comic book of The Flash, Eobard Thawne is the civilian alias for the Reverse-Flash/Professor Zoom.