SK is known for its pop-culture references. No wonder there are lots of them in missions as well.
Below, you can find the ones that I've identified at first glance (I don't mention obvious idioms like Pierce of Cake or In Cold Blood). I'm sure there are more though.
3-2 Shadow of the Beast
Reference to well known (but not so good IMO) computer game Shadow of the Beast.
4-3 Elemental My Dear
Reference to quote of famous Sherlock Holmes: Elementary, my dear Watson.
5-1 The Shadow Knows
Reference to the Shadow.
5-1 Work for Idle Hands
Reference to the idiom: The devil finds work for idle hands.
5-2 Time Enough at Last
Reference to the Twilight Zone episode called Time Enough at Last.
6-1 Axes of Evil
Reference to term used by George W. Bush to describe countries that he accused of helping terrorism.
8-2 The Great Escape
Reference to the film The Great Escape.
9-1 An Occurrence at Owlite Keep
Reference to the Twilight Zone episode called An Occurrence at Owl Creek Bridge.
9-2 Eye of the Needle
Reference to the book Eye of the Needle.
9-2 Alone in the Dark
Reference to one of the best game of my childhood - famous Alone in the Dark.
Man... I remember Alone in the Dark. I used to think that was some of the scariest junk I'd ever seen. Great times, great times...