Cisco Ramon had Babel Protocols built just in case the Flash ever went "dark" at S.T.A.R. Labs. This could be a reference to JLA: Tower of Babel, where Batman made contingency plans against the Justice League ever going rogue.
Ramsey's shapeshifted form is extremely similar to his official over-powered supervillain look in his one comic storyline at the time of the episode's release.
Joe's back is horribly torn up, possibly in reference to Jesse L. Martin's back injury that put him out of commission for most of the previous season.
Iris almost suffers the same fate as her pre-Crisis comics counterpart. The difference is that Barry prepares to stab her through the heart instead of through the head.
Cisco called the infected Barry "Dark Flash" as though he is based on his Negative Flash counterpart from the comic. "Dark Flash" is the nickname given to Eobard Thawne during Crisis on Earth-X, but he wasn't called that on screen, only in the concept art.