Archer

Ray: I mean, the mainframe thinks they're nuclear missile launches... This is a reference to the 1983 film WarGames, where a hacker initiates a nuclear war simulation on a military supercomputer, and almost starts World War III. The computer believes the simulation is real, and tries to retaliate against false Soviet attacks with nuclear missile launches.

Cyril: I've still got one bullet. Spelvin: Does he? Archer: Who am I, Count Bullets-ula? Like Dracula. That was bad. Come back to me. I can do better. This is a reference to the iconic character Dracula, first created by Bram Stoker in the 1897 novel of the same name.

Archer: Great, now he's going to be moping around like Droopy Dog on downers for the whole day. Droopy is a cartoon dog who moves and speaks slowly. He appeared in various MGM cartoons, and later in Turner Entertainment cartoons.

Archer: Way to go, Chokely Carmichael. This is a reference to Kwame Ture, a.k.a. Stokely Carmichael, an activist in the 1960s American Civil Rights Movement. He was a leader of the Black Panthers and popularized the term "Black Power".

The muffin in the briefcase gag is a reference to a Frisky Dingo episode "Meet Awesome-X" (a show by the same creator, Adam Reed).

Pam: How's the elevator supposed to work with a gillion pounds of frikkin' computers on it? Cheryl: Who am I, Elisha Otis?
Elisha Otis invented a safety device that prevented elevators from falling if the hoisting cable broke, and is remembered as a pioneer of elevator safety mechanisms.

Archer: Who am I, Alan Turing? Who's also from X-Men, remember?
Alan Turing was a famous English mathematician and computer scientist. He is not from the X-Men comic books/films, but Archer may be confusing him with Alan Cummings, the actor who played Nightcrawler in the films.

Krieger: (pounding the ground) No!! You maniac! You blew her up! Oh, damn you! God damn you all to hell!!
This is a reference to the ending of the film Planet of the Apes.