Actor Allusion: In "Blitzgiving", Jorge Garcia plays a cameo role. At one point someone asks for random numbers and he immediately shouts "4,8,15,16,23,42!" the Arc Numbers from LOST. His character is also cursed with being unlucky (as was his Lost character), and compares said curse with being on an island.
Adult Fear: Marshall's reaction to his father's sudden heart attack was sob-inducing because it was sudden and unexpected and it happens.
Amusing Injuries: Ted and Barney attempt to invoke this trope at Marshall's father's funeral.
Animal Stereotypes: Robin hangs out with a guy nicknamed Scooby in "A Change of Heart" who is extremely dog-like. He is played by the actor who was Fred in the reboot movies.
Arc Words: "Things have to fall down to make way for new things" and "New is always better".
Aside Glance: in "The Mermaid Theory". Future!Ted can't remember why Barney & Lily were fighting and they "freeze" while they are shouting while he tries to figure out what was going on that day. They then awkwardly look at the screen and surreptitiously check their watches.
Attention Deficit... Ooh, Shiny!: Barney's ADD comes up a few times. After a phone call with Marshall, Barney trashes his office in a violent rage, only to discover that Robin is staring at him from the doorway. Shocked, he asks her how long she's been there. Turns out he'd been talking to her before randomly calling Marshall, and completely forgot she was even there.
Upon learning the origin of The Captain's name when they meet, Ted introduces himself as Galactic President Superstar Mc Aweseomeville - and the Captain addresses him that way for the rest of the night.
Back for the Dead: Marshall's dad is made much more important shortly before he dies.
Robin: The way that she bats her eyelashes and shakes her tail feathers in his face. Oh, she wants it.
Also, because this is what they're describing, Ted and Zoey.
The B Grade: In "Subway Wars". Architecture professor Ted finds out about a website where students can rate their teacher. He checks it out and finds he's received dozens of glowing reviews. The one that he obsesses over calls him "boring".
Borrowed Catchphrase: Barney fires off an absolutely epic string of actual reality show dismissal catchphrases in an episode.
Break the Cutie: Season 6 seems to enjoy throwing these at Barney, especially at the end of an episode.
Brick Joke: "Legen... wait for it... and I'll send you the rest in an inter office memo because we FREAKING WORK TOGETHER!" Their next scene together, Ted gets an "important inter-office memo" reading "DARY."
The Cameo: New Yorkers see Maury Povich all the time.
Catchphrase Interruptus: In "Natural History," the night guard begins to describe Barney's childhood escapade as "Legen—" and his phone rings. He says, "hold on," turns off the ringer, and completes the catchphrase.
Cut off by a sneeze in "A Change of Heart." Oddly enough, he doesn't finish it afterwards.
Chair Reveal: Barney does this again in 'Architect of Destruction'.
Chekhov's Gun: Marshall's phone remains uncharged at the end of the episode "Bad News." It's important for the next episode, as his father's last words were on that phone and he didn't know until the funeral.
Chekhov's Acoustic Sweet Spot: naturally someone overhears something important thanks to the shape of the dome and being on said sweet spot. Very straight example.
In the episode "Subway Wars" Barney's ability to tell if a girl has been crying is introduced well before he needs it to help Robin.
Cloud Cuckoo Lander: Barney's suggestion to Ted as to what the design for the new GNB building should be "a gigantic rooftop ring of fire that you can jump through on a motorcycle." Ted tweaks it to a rooftop patio instead where you can eat your bag lunch. Barney is just as excited about the patio, if not more.
Also his answer to Nora when she asks how many kids he would want, and he responds with "Three. One of each".
Color-Coded Characters: In "Oh Honey," the characters are dressed in colors matching characters in Clue. Ted is dressed in purples (Professor Plum), Barney always wore green somewhere (Mr. Green), Robin dressed in blue (Mrs. Peacock), Zoey wore white (Mrs. White), and Honey wore red (Miss Scarlett).
Indicative of Ships- During the phone scene Lily wears a pink shirt under a grey sweater and Marshalls shirt is grey and pink. Ted's purple shirts have white accents such as the purple and white striped tie, or a white undershirt and Zoey wears white.
Continuity Nod: In "Bad News" Barney wears Ted's Sensory Depriver from season 2's "Monday Night Football". Also, Robin has to work together with her co-host from the first season.
In "Canning Randy", Lily mentions "that '98 Taurus that's always parked outside with the really annoying alarm", which Ted and Robin then imitate. It sounds exactly like the one from "Luck Penny".
After finding the latest Robin Sparkles show called "Space Teens", Barney thinks it's a porno and prepares to slap the bejeezus out of Marshall who is already cringing: a nod to the second season episode, "Slap Bet."
In "Oh, Honey", the Loch Ness Monster poster in Marshall's childhood room.
"Canning Randy". Ted says that he is in favor of the Arcadian being torn down. Zoey starts to act like a complete snob. So to try to make it up to his students, he gives them candy and makes a mix CD. Zoey's response? To take his entire class and turn it against him.
Enforced Method Acting: Jason Segel was not told that the bad news in "Bad News" was his character's father dying until the words came out of Alyson Hannigan's mouth while shooting the final scene (which was just one take). He also improvised the line "I'm not ready for this."
Foreshadowing: Season 6 drops a big one. One of Ted's stipulations for Cindy to make it up to him is to set him up with one of her friends...
Barney in the first episode of Season 6 states that if he ever had his father's phone number, he would never not talk to him. Second episode, Barney's mother offers him the contact information of his real father, which he tears up saying his mom was father enough for him.
In a flashback that takes place after Ted gets married to the mother, he states in passing that his relationship with Zoey ended badly.
A subtler bit of foreshadowing occurs in the episode where Ted and Zoey first got together. In that episode she introduces Ted to her cousin, whom Future!Ted calls "Honey" because he's forgotten her real name. If Zoey were the mother, Ted should've been able to remember Honey's real name.
Another big one was dropped at the end of the Season 6 finale. The episode teased a possible reconnection between Robin and Barney, only for them to decide it isn't a good idea. Barney runs in to Nora, and we are teased with a reconnection between those two. We flash forward a bit to learn that Barney is getting married, with Ted as his best man, though who Barney marries is not revealed. Word of God says that Season 7 will partly focus on learning who it is Barney will marry, and that it is at that wedding that Ted meets The Mother.
In an early episode, Ted annoys some people on the bus with archictural information on various buildings, among them the Arcadian, which will later become central to the season's story.
Very subtle one in season 4, Marshall says that in 3-5 years, he'll be carving the Thanksgiving turkey with a lightsaber. The stinger of the episode ends with him doing that, with the subtitle of "Three to five years later" Marshall is shown doing just that. But before he does, he says a few words to Lily and his mother. But not his father, who dies two years later... before this scene would take place.
In the eighth episode, Barney's story about destroying the whale while at the museum with his "Uncle Jerry". Think about it, why would Barney's mom let some random boyfriend take her son anywhere?
Gilligan Cut: Barney states that the entire gang will be helping him clean out his mother's house this weekend. No one is convinced and states that his schmoozing powers may work on unaware girls but will never work on his friends. Cut to everyone helping to clean Barney's mother's house and Lily wondering how he did that.
Groin Attack: Ted and Barney try to get Marshal to laugh at his father's funeral by showing him video's of people getting hit in the groin. When that fails, Barney hits Ted in the groin, which also fails.
Heads, Tails, Edge: In "Blitzgiving", once Barney inherits the curse of "The Blitz" which makes awesome things happen just as he isn't there to see them, the original Blitz flips a coin while Barney is out of the room and it lands on its edge. It falls over just as Barney returns.
Honorary Uncle: Barney tells Robin of the time when "Uncle Jerry" took him to the Museum of Natural History. Everyone understands that the guy was just one of Barney's mother's many boyfriends and had no actual relation to Barney. However, at the end of the episode we find out that Jerry might actually be Barney's real father.
Imagine Spot: Barney doesn't actually walk into the restaurant to win Nora back at the end of "A Change of Heart".
Innocent Innuendo: In the third Robin Sparkles educational special, she and Jessica Glitter talk about their beavers and Alan Thicke asks a math question about how much wood is needed to keep the beavers well fed all weekend long. Ted and Barney nearly have aneurysms.
Ted: She didn't see us high-six did she? Robin: No. Barney: Good. That was pretty lame. Ted: Yeah, let's never do that again.
Line-of-Sight Name: In the episode "Canning Randy," Robin looks at the bill and the pepper shaker on the restaurant table and claims that the man she slept with was called "Bill Pepper." Lily, not fooled, inquires if Bill knows "Fork Napkin."
Letting the Air Out of the Band: In "Bad News", they watch a short clip of a bagpiper getting hit in the nuts by a low-flying seagull, and the bagpipe sound slowly deflates afterward.
Lovely Assistant: Parodied in "False Positive", when news anchor Robin suffers a crisis of confidence and auditions to be the "coin-flip bimbo" (or "currency rotation specialist") on Million-Dollar Heads Or Tails.
Manly Tears: Marshall when he learns that his father died.
Mood Whiplash: In "Bad News", Marshall gets tested to see if he can even get Lily pregnant. The doctor comes in to say that his sperm aren't fertile... before Marshall rips the beard off of the doctor to reveal that he's Barney. Then the real doctor comes in and says that Marshall is fertile. Later he celebrates at the bar, leaves to call his dad to tell him the good news... to run into Lily leaving a cab saying his dad died of a heart attack. Ouch.
No Matter How Much I Beg: Robin, reeling over a breakup, warns friend (and ex-boyfriend) Ted that some time in the future she will attempt rebound sex with him, and makes him promise to resist her advances. By the time she makes her move, she's such an emotional (and physical) wreck that Ted finds resisting very easy.
Noodle Implements: We still don't know what Barney does, but we do know he has a lot of keys.
Noodle Incident: Barney blackmailed the gang into making him look good to Nora by his knowledge of embarrassing things that happened to them. Only Marshall's eating a calzone he dropped on the ground was explained. What happened to the hamster in Lily's class, Robin's Mr. T dream and Ted's Thermos is not explained.
Numerological Motif: Various props in the season 6 episode "Bad News" count down from 50 to 1 until the announcement that Marshall's father has had a fatal heart attack.
Open-Minded Parent: Barney's mum is a lot more accepting of his lifestyle than Barney was expecting, mostly because she was exactly like him when she was younger.
Perfectly Cromulent Word: Marshall has been using these to avoid lying to Lily. If it's not a word, it can't be false, right? Also, Barney likes to make up words to sound more awesome.
Promoted Fangirl: In interviews Jennifer Morrison has stated she was a huge fan of the show and actively campaigned to get her part.
Rage Against the Heavens: Marshall has one. At the end of the episode Last Words Marshall rants to God about how unfair the whole situation is with his father's untimely death... good thing his dad pulls through in the end.
"The Reason You Suck" Speech: In "False Positive" everyone except Ted had plans on doing something significant with their lives when Lily and Marshall briefly believe Lily is pregnant. When they find it was a false positive they begin backtracking on their plans: Lily and Marshall panicked and decided to wait a little longer on having a family, Barney bought a diamond pleated suit instead of giving his Christmas bonus to charity like he promised and Robin backed down from a news company she wanted to work for (room to grow but did not start out where she wanted to be). Ted was so disgusted with their behavior he proceeded to call them out for wimping out of what they really want just because they knew the path was going to be hard.
Red Herring: At the beginning of the season Ted says he found the mother at the day of the wedding that he was best man at. Ted reaffirms his friendship with his old friend Punchy and becomes the best man at his wedding. At the end of the season the Groom turns out to be Barney.
Reflexive Response: When Lily announces that she's pregnant in False Positive, Barney immediately screams "I've never slept with that woman before in my life!"
Shout-Out: In "Canning Randy" there is a reference to the Godfather's dead horse head scene.
In "Glitter" when Punchy shows up he says ,"Feels like you're dreaming? Well check your totem, bro!" Referring to Inception
In the episode "Blitzgiving" Steve Henry (played by the same actor as Hurley from Lost) shouted out the numbers 4 8 15 16 23 42 and how he was stuck on an island.
In "False Positive", Barney plans to get a very expensive suit called the DiBiase.
In "Baby Talk" the first name Lily suggests for their daughter is Tara, a reference to the girlfriend of Alyson Hannigan's character from Buffy the Vampire Slayer.
"Blitzgiving" has a pair of Buffy moments, both from "Hush": The catchphrase "The Gentlemen" refers to the villains in that episode, and the special effect of the Blitz passing from one person to the other is the same as the effect used when the Gentlemen steal somebody's voice.
Show Within a Show: Alex Trebek hosts "Million Dollar Heads Or Tails" (which had been hosted in season 4 by Regis Philbin).
The Captain: I daresay Scylla and Charibdis could not have torn us asunder: we had great big boners for each other.
Soundtrack Dissonance: While discussing losing a potential friendship with Lily, Jessica Glitter, Robin's ex-BFF, is playing an organ for a hockey game. The happy organ music being played (and the Pavlovian responses to certain tunes) gives a comical contrast to the seriousness of the discussion.
Spit Take: Barney and Ted both have one when the first words said in the section of the third Robin Sparkles special they're watching are "How's your beaver?"
Happens to Barney in 'Architect of Destruction' when Ted told him and the gang that he didn't tell Zoey that he's the architect of the new GNB building and instead tells her that he's a veterinarian.
Variations on a Theme Song: Episode 21, After Barney claims the group is in a band during the cold open, the theme song is sung by the main cast, instead of the usual title sequence.
Wham Episode: "Natural History": One minute it seems like a fun episode about Barney and Robin touching things they aren't supposed to at the museum and the next thing you know, Barney learns the truth about his father.
"Bad News": One moment, we're celebrating with Marshall about his "strong swimmers," next moment he learns that his father has died.
The season six finale "Challenge Accepted" gave us two wham moments. We find out that Lily is pregnant and does not in fact have food poisoning, and as Ted performs his Best Man duties at a wedding, it is revealed that the groom is actually Barney.
Lily: (in tears) Marshall, something's happened... your dad had a heart attack...h-he didn't make it...
"Natural History" when Barney finally learned the identity of his father just after he gets over it.
Guard: Stinson was reprimanded and returned to the custody of his father, Jerome Whittaker.
After Barney has been acting weird about the fact that his biological father isn't cool anymore:
Barney: You're lame, okay? You're just some lame suburban dad.
Jerome: Why does that make you so mad?
Barney: Because if you were gonna be some lame suburban dad, why couldn't you have been that for me?!
What Do You Mean, It's for Kids?: In-universe, Robin insists that "Space Teens" is an educational show for kids, despite two girls wrestling over a suggestively-shaped joystick, followed by "The Beaver Song."
What the Hell, Hero?: Lily gives one to Barney for lying to Nora, despite their feelings for each other and her being quite possibly the most decent girl Barney has ever met.
Who's on First?: In "Hopeless", the entire gang and Barney's father engage in this when trying to figure out which club to go to. Barney's father even lampshades the conversation by uttering lines from the original skit... and then the lampshading is incorporated into the joke.
"Okay is Lame. Gay bar."
Why Would Anyone Take Her Back: In-Universe, the rest of the group ask Ted when he considers getting back together with Zoey at the end of season 6 why he would, because she tried to destroy his career, manipulated him, lied to him, and secretly taped his conversations so that she could constantly screw him over. This makes Ted realize that they're right and that she is not worth it.
Younger than She Looks: At the funeral of Marshall's father, Robin gives booze to a girl that looks at least in her mid 20's, later it's revealed that she's just a very tall 15 year old, much to the surprise of Robin, and Barney, who immediately returns the phone number she had given him.
Yuppie Couple: Taken to the ultimate extreme in "Subway Wars" where the gang race downtown to see Woody Allen at a restaurant after mentioning the fact that they see Maury Povich all the time. In a virtually Real Time episode every character runs into Povich in completely different locations.