On the BBC show, Kingdom, starring Stephen Fry, there’s an episode where a father is telling his daughter to go off to college and that he’ll be okay without her. He says something like, “Maybe I’ll get a butler” and then the camera focuses on Stephen Fry for no reason (reference to Fry’s character in Jeeves and Wooster who was a butler).
In *Epic Movie *(not that I’ve, uh, seen it), Edward says “White Castle? I feel like I’ve been there before.” in response to the White Bitch showing him her white castle, which is an actual White Castle restaurant (in case you’re really too stupid to catch the reference). Edward is played by Kal Penn, who was Kumar in Harold and Kumar Go To White Castle.
I seem to remember a scene in the new Battlestar Galactica where someone calls out “Apollo” and Richard Hatch (Apollo from the original series, now playing a different character) turns in recognition.
Nothing about Epic Movie should be considered witty or clever.
In a recent episode of Bones (starring David Boreanaz, although he is offscreen at this point), one of the characters admits to being a big geek, and being into ‘you know, Star Trek, Buffy etc.’
In the movie “Drillbit Taylor” the children of the movie are interviewing people to become their bodyguards. One of the interviewees is Adam Baldwin, and his line is something like, “Kids hiring a bodyguard to take care of a bully? Stupidest thing I ever heard.” He is wearing the army jacket he wore in the movie “My Bodyguard.”
Boston Legal had lots of these.
Denny Crane (William Shatner)'s cell phone chirps like an old-school communicator.
Denny also announces “I had my own spaceship!”
Denny tells Paul (Rene Auberjonois) “I’m the captain!” during an argument.
Denny’s new wife wants him to move to Hawaii with her. He asks “What am I supposed to do, beam to Boston every morning?”
Alan describes sea lice as “cling-ons” and Denny, looking surly repeats “Klingons?!”
Denny tells a crowd that he has an Emmy.
Denny responds to a question from John Laroquette by telling him “I lied.” This is a reference to the same response to Laroquette’s character Maltz in Star Trek: The Search for Spock.
I remember seeing a couple Blackadder references in House but the only specific one I can remember is House saying something about a cunning plan.
House also had Blackadder in his Tivo queue.
I as just watching Thunderball, which brought another to mind. As Sean Connery, as Bond, is leabving the Heath Retreat at Shrublands, the nurse he’s seduced says, “Can we meet again, sometime, someplace?”
To which Connery responds,“Another Time. Another Place.”
Another Time, Another Place was a 1958 film in which Connery starred as a BBC war correspondent:
The SG-1 episode “200” has a brilliant parody of Farscape in it, Claudia Black played Aeryn Sun in 'Scape, and Ben Browder played John Crichton (in the 200 'Scape parody clip Browder played Stark though)
Vala-Aeryn Sun
Jackson- John Crichton
Mitchell- Stark
Teal’c- D’argo
Carter- Chiana
Thor- Rygel
It’s an even better reference when you realize that Aeryn and John were romantically entangled in 'Scape, and Vala and Jackson appear to be in SG1
…and the “I have no idea what that is” comment at the end of the clip plays off the “poor ratings” 'Scape was getting near the end of Season 4 because Bonnie Hammer (BOO!!) and her brainless Sci-Fi channel minions were frelling around with 'Scape’s time slot
the entire 200 episode is a hilarious send-up of Sci-Fi and fantasy
In an all time great missed opportunity to do this, someone mentioned Ted Bundy to Agent Gibbs (Mark Harmon) who played Bundy in a TV movie. Gibbs did not say “You cannot tell me anything about Bundy that I don’t know” or some such comment.
Another great missed opportunity: Pepper Mill is a BIG fan of Scott Bakula in anything, but especially Quantum Leap. Of course, she loved him as Jonathan Archer in Enterprise as well.
At the end of the pilot episode of Enterprise, Captain Archer is finally rescued by the not-operating-until-then Transporter.As she pointed out, it would’ve been perfect if he’d then sighed heavily and emitted a Sam Beckett-ish “Oh, boy!”
But, of course, they didn’t. Probably didn’t want to pollute the series with references to other stuff.
But all the fans were thinking it.
In the movie Harold and Kumar Escape From Guantanamo Bay, Neal Patrick Harris plays himself. There are several moments where other characters, and he himself, confuse him with other characters he’s played. (For most of his appearance he’s blitzed out on whiskey, acid, mushrooms or all three)
I’m watching Enterprise now, about halfway through the third season, and I keep my fingers crossed every single episode for an “oh, boy.” Don’t harsh my hopes. 
I was tickled in the episode I cited above to hear references both to Ceti Alpha V and the Mutara sector.
Speaking of Enterprise and Quantum Leap, Dean Stockwell appeared in one episode, and he apparently carried a handheld computer that looked and sounded like the one he carried in QL:
I was very upset that not once during the entire series did they have him say “Oh, boy.”
It just wasn’t right.
There was an episode of Married with Children with two scenes of teople following Jefferson D’Arcy (Ted McGinley) around and screaming. The first group was screaming about “Happy Days” and the second about “The Love Boat.”
NCIS Season 4 episode called Escape, Mcgee remarks that the character played by Hal Holbrook has a first edition of Huckleberry Finn–a reference to Holbrook’s one-man show where he plays Mark Twain.
The Nanny had an episode where Mr. Sheffield (Charles Shannessey) was trying to get a soap star (Steve Nichols) to do his new show. The star agreed provided he could go on a date with the Nanny.
The star starts to get fresh with her in the limo. Fran says she’s going to report him to Soap Opera Digest. The guy puts on a black eye patch and announces he is really his character’s evil twin.
Nichols played Steven “Patch” Johnson on Days our Lives opposite Shannesey’s Shane Donovan for years.
The Nanny also brought back Bobbie Flechman, Fran’s role from the movie “This is Spinal Tap.” Not a stretch, sinch Sheffield is a Brit in musical theatre. When Fran thinks their relationship might have been romantic, she kidnaps Fleckman and then impersonates her. So Fran Drescher played Fran Fine imitating Bobbie Fleckman. Did a good job too.
In the short lived TV series Harper Valley PTA, Stella Johnson (Barbara Eden) wore a Jeannie outfit.