Sam and Fiona approach a group of con artists while under the guise of federal agents who had been monitoring them. Sam introduces himself and Fi as detectives Cagney & Lacey, alluding to costar Sharon Gless.
Additionally, in the second season Fiona starts dating a man named Campbell. In one episode, a conversation between Fiona and Sam takes place, with Fiona commenting on how good-looking a particular man is, to which Sam (played by Bruce Campbell) replies, "Well, he's no Campbell."
Michael also makes contact with a Libyan operative named Anwar in one episode.
Inverted in a "Signals and Codes" where the client of the week was played by an actor named Michael Weston.
In one episode, Sam and Barry are discussing people who only use one name, and Sam says "Spider-Man" as an example. Bruce Campbell has a cameo in all three of the Spider-Man movies.
And in the winter premiere of season 3, Tyne Daly guest stars.
Word of God mentions that as a general rule, they write characters with a specific actor in mind. This is in part due to the need to quickly establish characters and chemistry (see the above Tyne Daly instance) as it is just having fun.
There was also "False Flag", where Fi said Sam's bulletproof vest smells like Old Spice and bourbon. Bruce Campbell is a spokesperson for Old Spice.
In one episode, Sam is doing surveillance on Carla, who takes time to swim. Commenting on her ability, Sam says: "The woman is a machine." Carla's actress, Tricia Helfer, played a robot on Battlestar Galactica.
In 5x6, Sam compliments Mike on his chin. Mike instantly turns to face Sam, seemingly very surprised, and notes that it means a lot coming from Sam. Bruce Campbell (Sam) really is known for his chin among other things — he even titled the book he authored after his chin.
A recent episode showed Gabrielle Anwar once again getting to tango.
John C. McGinley plays Michael's former CIA mentor Tom Card. References to McGinley's role as Dr. Cox on Scrubs abound: among other things, Card displays expasperation and impatience with his young protege, he does a ton of Deadpan Snarking, and he even does Dr. Cox's frustrated whistle in one scene.
Barry the money launderer refers to Sam's shotgun as his "boomstick."
In 3x04 "Fearless Leader," a pack of "Morley" brand cigarettes show up — the favorite choice of the Cigarette-Smoking Man. Also in that episode, the Villain of the Week is named after actor (and frequent episode director) Tim Matheson.
Morleys are actually seen frequently on the show. They're Maddie's preferred brand, and many of the smoking villains are seen with them as well. Seems appropriate, since this show is also about a government employee trying to unravel a massive conspiracy...
A hotel at the end of season 2 is named after William Wages (executive producer?) and the VOTW from "The Hunter" is named for Jeremiah Chechik, director.
Perhaps a subtle or unintentional one but in Season 3 finale while fighting, Simon takes Michael from behind and slams him repeatedly against a wall. The short sequence uses the much of the same cinematography as the fight between the T-800 and T-1000 from Terminator 2. Earlier in the episode, Simon walks out from behind the heat haze of an explosion in a police outfit — again, sharing similar cinematography to what the Terminator series of works have used prior. Garrett Dillahunt (Simon) previously played a Terminator and A.I. in The Sarah Connor Chronicles.
Simon and Fiona also got to talk to Olivia Benson.
Max and Strickler were patients at Seatle Grace hospital, agent Pierce was a nurse there.
In "Where There's Smoke", a gang of kidnappers is led by two brothers named Eddy and Jacob.
In "Breach of Faith", Sam mentions how he really wanted a Red Rider BB rifle as a kid.
In "Out of the Fire", Sam dryly quips to Brennen: "Don't take my silence for stupidity. I was just trying to kill you with my mind".
When buying a phone off of a child in Panama, Jesse's cover name is Seņor Tibbs.
In "Down & Out", the fake ID Sam is given as his alias is "Randy Weems", and he asks what kind of name Randy Weems is. It's the name (or the nickname) of a snivelling little tattle-tale.
In "A New Deal", while bare-knuckled boxing early in the episode, Michael gets punched and knocked up into the air in a manner very reminiscent of an iconic scene in Snatch.
In "Last Rites" Nate and Sam are pretending to be CDC field agents when a subject walks in on Nate opening a phone receiver to bug it. The excuse to cover for this? Nate's handling the very bacteria the CDC was looking for — in other words, he's a phone sanitizer.
In the tie-in novel, "The Fix", multiple shoutouts are made: