When Cecile mentioned not receiving a totem from her grandmother, it is a reference to Vixen (Mari McCabe) who wears a totem around her neck that gives her the abilities of any animal.
The theory that those shrunk will explode after a certain time may be a reference to Ray Palmer's abilities; in the comics, Palmer has stated that he is the only person who can safely shrink with his abilities, as anyone else who shrinks with him will explode after a certain amount of time (initially two minutes, but later extended to an hour).
When Harry talks about "embiggening" Cisco and Ralph, it is a reference to the statue of Jebediah Springfield in The Simpsons. The inscription of the stature reads "a noble spirit embiggins the smallest man". In the Simpsons, this is later challenged by one teacher, who claims that "embiggen" isn't a real word, to which another teacher responds, "it's a perfectly cromulent word." The joke here is that "embiggen" is, in fact, a word (although an archaic one) and "cromulent" is not. This, too, is later referenced by Iris.
Sylbert Rundine / Dwarfstar is a supervillain and the arch-enemy of Ryan Choi, the second Atom. He first appeared in All-New Atom #2 (October 2006).
Danielle Panabaker (Caitlin Snow) and Derek Mears (Sylbert Rundine / Dwarfstar) both starred in Friday the 13th (2009) in which they played Jenna and Jason Voorhees respectively.