To V for Vendetta, or at the very least Guy Fawkes Day: Liber8 leader Edouard Kagame opens the series premiere with a scene where he outlines the group's manifesto, calls for a rebellion, then blows up a large building. The date? November 5th, 2076.
After Kiera explains a murdered scientist's revolutionary work on matter/antimatter power generation, Carlos comments that she must have "watched too much Star Trek as a kid".note In case you missed the actual connection, Rachel Nichols played Gaila, the Green-Skinned Space Babe Orion cadet, in the 2009 film.
In one episode, Kiera and Carlos track down Herbert George, who is a student at Faber College.note Fridge Logic: Heck of a coincidence that there had been a student of that name.
"Second Truths" has a reference to Breaking Bad: Emily jokingly refers to Alec as "Heisenberg". Alec continues the reference by reassuring her he means cooking food in his lab.
Does Section 6 remind anybody else of Public Security Section 9? Maybe that's where Alex got the cover story.
Near the beginning of the season 1 finale, Sonya gives Kagame a copy of "A Tale of Two Cities" as a birthday present — the same gift that Spock gave to Kirk near the beginning of The Wrath of Khan.