Legend of Legaia (PS1)

Cross-Series (Alundra): One of the songs from Alundra also appears in Legend of Legaia. The sad theme for both games. (Credit: Oddeye)
Status: TRUE: The song being referred to here is called "Cara's Theme" on the PSF soundtrack of Legaia, and it's identical to the one called "Requiem" on Alundra's PSF (called "Dust to Dust" in Alundra's in-game Sound Test). Here's a (PSF File) for proof, but I'm only putting up one because the PSF's for both games are identical.

Cross-Series (Alundra): There's another song that appears in both of Legaia's and Alundra's PSF soundtracks! It's called "Excitement 2" on Alundra's and "Unknown" on Legaia's. Here's a (PSF File) of it, but I don't know what it's used for in either game. I only finished Alundra once, and I don't remember this piece, though when I heard it on the Legaia soundtrack, I immediately recognized it as one I'd heard in Alundra's soundtrack.
Status: TRUE: Verified by FO.

Legend of Mana (PS1)

Cross-Series (Various): If certain requirements are met, you can have a Chocobo (from the Final Fantasy games) as a pet monster, as well as a sword from SaGa Frontier 2. (Credit: Ace Whatever)
Status: Unverified

Legend of the Mystical Ninja, The (SNES)

Cross-Series (Kid Dracula): There's a Kid Dracula head item hidden on the side of the HoroHoro Temple in the first town.
Status: TRUE: (Screenshot) proves it.

Cross-Series (Gradius): The arcade house has the first level of Gradius. (Credit: Crawl and 1000)
Status: TRUE: Verified by FO.

Cross-Series (Wai Wai World): The purple-haired, long-eared (or are those horns?) girl that appears on the televisions in the arcades to ask you what game you want to play is none other than Konami Girl, costar of the Famicom game Wai Wai World. (Credit: Dire 51)
Status: TRUE: Verified by FO. Source: The OPCFG.

Legend of Zelda, The (NES)

Cross-Series (Clu Clu Land): The rupee was a graphic originally used in Clu Clu Land. (Credit: Shadow Villgust)
Status: TRUE: Screenshots prove it: (Clu Clu Land Rupee) (Legend of Zelda Rupee)

Legend of Zelda: A Link to the Past, The (SNES)

Cross-Series (Super Mario Bros.): Mario's head appears in paintings on walls.
Status: TRUE: (Screenshot) proves it.

Cross-Series (Super Mario Bros. 3): There are Chain Chomps from Super Mario Bros. 3 in Turtle Rock Dungeon.
Status: TRUE: (Screenshot) proves it. On side note, doesn't it seem like Turtle Rock is somehow connected to the Mario Universe? First of all, it's shaped like a turtle (Koopa), it has the Chain Chomps, and you go through pipes while inside of it (there is no place else in the game where you do this). Also, the enemies that surround its Light World counterpart look similar to Para-Goombas.

Movie (The Wizard of Oz): Possible Wizard of Oz reference: The sign that's next to the sleeping man in the desert says, "Pay no attention to the man sleeping by this sign", which is a lot like the line near the end of The Wizard of Oz where the Wizard says, "Pay no attention to that man behind the curtain!" (Screenshot)
Status: Coincidence?: That line is so famous, I'd be really surprised if this wasn't intentional.

Miscellaneous: There is a very well-hidden secret room with the name "Chris Houlihan" written on a wall tile. He is the winner of a Nintendo Power contest to have his name featured in a game. (Credit: Kairobi King)
Status: TRUE: Verified by FO. Source: Nintendo Power.

Legend of Zelda: Link's Awakening, The (GB)

Cross-Series (Super Mario Bros.): Goombas and Pirahna Plants from the Super Mario Bros. games appear in the underground tunnels that connect areas of the dungeons. Interestingly enough, while the Goombas can be killed by the sword or other methods, only stomping them, a la Mario, will give you a heart. (Credit: Flying Omelette & Mike Waters)
Status: TRUE: Verified by FO.

Cross-Series (SimCity): Mr. Write is Dr. Wright from the SNES version of SimCity. The music heard in both Mr. Write's and the Goat Lady's houses is Dr. Wright's theme from SimCity. (Credit: Flying Omelette & Andrew Rae)
Status: TRUE: Verified by FO.

Cross-Series (Super Mario Bros.): Tarin looks like Mario, he hunts for mushrooms in the woods, and turns into a Raccoon after eating a "strange leaf". The man in the henhouse looks like Luigi. The picture that the Goat Lady sends to Mr. Write is a picture of Princess Toadstool (Peach). Bowwow, the dog in Mabe Village, is a Chain Chomp from Super Mario Bros. 3.
Status: TRUE: Verified by FO.

Cross-Series (Kirby): There's an enemy called Anti-Kirby in one of the palaces that looks like Kirby, and it even tries to inhale you. (Credit: Flying Omelette & Timothy Barta)
Status: TRUE: Verified by FO.

Cross-Series (Super Mario Bros. 2): The Frog King that teaches you the "Frog Song of Soul" is Wart from Super Mario Bros. 2/Doki Doki Panic.
Status: TRUE: Verified by FO.

Console (N64): If you throw magic powder on one of those enemies that looks like a dancing pickle, it changes form, and if you talk to it, it says something like, "It can display thousands of polygons", which might either be a reference to the Super FX Chip or the N64, if the N64 was in development at the time Link's Awakening was made.
Status: TRUE: Verified by FO.

Cross-Series (Super Mario World): In the crane game, you can get a Yoshi Doll as a prize. (Credit: Codie Martin)
Status: TRUE: Verified by FO.

Cross-Series (Kaeru no Tame ni Kane ha Naru): Richard is from a Japanese Game Boy game called "Kaeru no Tame ni Kane ha Naru". Kaeru is Japanese for "Frog", which explains the frogs in his house. (Credit: Mark Kelly)
Status: TRUE: Verified by FO. Source: Nintendo Database.

Cross-Series (Super Mario Bros.): Other Mario enemies that appear in the game include Boo Buddy, Blooper, Pokey, Piranha Plant, Cheep Cheep, Goomba, Shy Guy. All have their Mario names except Shy Guy who is called "Mask Mimic". The Japanese version does use his Mario name, though. (Credit: Mark Kelly)
Status: TRUE: Verified by FO.

Cross-Series (Mario Paint): In the Japanese version, enter your name as TOTAKEKE (in Japanese Katakana). The background music will change to the strange tune from Mario Paint, Kazumi Totaka's signature tune. In Richard's house let the music loop a few times and it changes to a different version of Kazumi Totaka's signature tune. (Credit: Mark Kelly)
Status: TRUE: Verified by FO. Source: Nintendo Database.

Legend of Zelda: Majora's Mask, The (N64)

Music: You play the song "The Ballad of the Wind Fish" in the milk bar. The song title comes from Link's Awakening. (Credit: Bomberguy221)
Status: TRUE: Verified by www.vgmusic.com.

Cross-Series (Super Mario Bros.): One of the masks that the mask salesman has on his backpack looks like Mario. (Credit: Isaac)
Status: Unverified

Legend of Zelda: Ocarina of Time, The (N64)

Cross-Series (Super Mario Bros.): Talon and Ingo look like Mario and Luigi. Malon might possibly be based on Princess Toadstool (Peach), and she is wearing a Bowser-head brooch. There are also pictures of Mario and other characters from the Mario games behind a window in Hyrule Castle Courtyard.
Status: TRUE: Verified by FO.

Character Cameos: Malon and Talon of 64 and the GBC Zelda games are clearly based on Marin and Tarin of Link's Awakening. I'm not even sure why they bothered to renamed them, as the characters are so alike in every way: Malon, young girl, crush on Link, sings; Talon, her lazy father, sleeps all the time. (Credit: Aaron Campbell)
Status: TRUE: Verified by FO. Perhaps Nintendo renamed them as a way of explaining how these characters, who existed only in a dream, ended up being in the real Hylian world after all.

Cross-Series (Super Mario 64): A sign on the second floor of the Dodongo's cavern is printed on a stone tablet rather than a usual sign. The bizarre texture used on the tablet is the same texture used on the fountain in the castle garden in Super Mario 64. (Credit: Mark Kelly)
Status: TRUE: Verified by FO. Note that this is the same texture tile that caused that whole "Luigi is in Super Mario 64" rumor years ago.

Legend of Zelda: Oracle of Seasons, The (GBC)

Cross-Series (Super Mario Bros.): The Cheep-Cheeps from Super Mario Bros. are in Zelda: Oracle of Seasons. (Credit: JG Shady)
Status: Unverified

Legend of Zelda: The Wind Waker, The (GCN)

Cross-Series (Luigi's Mansion): The pirate Mako appears to have been based on Professor E. Gadd from Luigi's Mansion. (Credit: BGBW & Fenrir X)
Status: TRUE: (Picture) proves it.

Leisure Suit Larry in the Land of the Lounge Lizards (PC)

Real Place (Las Vegas): The entire game takes place in a city called "Lost Wages", which is an obvious parody of the real-life city, Las Vegas. (Credit: SlyDante)
Status: Unverified

Mythology (Biblical): In order to get Eve to talk to you, you have to give her an apple, an obvious reference to the biblical legend of Adam & Eve. (Credit: SlyDante)
Status: Unverified

Programmers: After you beat the game, Sierra founder Ken Williams will come out to congratulate you, and in the VGA versions, he'll make advertisements for Leisure Suit Larry games 2, 3, & 5. (Credit: SlyDante)
Status: Unverified

Leisure Suit Larry 2: Goes Looking For Love in Several Wrong Places (PC)

Specific Reference: At the beginning of the game, Eve sics a dog on you that urinates on Larry, much like the dog in the first game. The game even says the dog looks familiar. (Credit: SlyDante)
Status: Unverified

Products (Big Gulp): The Quikie Mart convenience store sells you a drink called a "Grotesque Gulp", a parody of the Big Gulps sold at the real-life 7-11 convenience stores. (Credit: SlyDante)
Status: Unverified

Cross-Series (Police Quest): If you take a peek through the hole in the fence behind Quikie Mart, you'll be told that you see a bunch of people playing Police Quest, another Sierra adventure game. (Credit: SlyDante)
Status: Unverified

Programmers: Two of the people who eat at the restaurant in the jungle are Sierra founders Ken and Roberta Williams. Chief Keneewauwau, the chief of the tribe on Nontoonyt Island looks an awful lot like Sierra founder Ken Williams. (Credit: SlyDante)
Status: Unverified

Miscellaneous: At the airport, Larry encounters some cult members called the Hairy Krishnas, who are parodies of the Hare Krishna religious group. (Credit: SlyDante)
Status: Unverified

Leisure Suit Larry 3: Passionate Patti in Pursuit of the Pulsating Pectorals (PC)

Specific Reference: Look at the statue at the beginning of the game: It's dedicated to Larry for saving Nontoonyt Island, as in Leisure Suit Larry 2. (Credit: SlyDante)
Status: Unverified

Programmers: Chief Keneewauwau shows up again, and he still looks like Ken Williams. (Credit: SlyDante)
Status: Unverified

Real Place (Chippendales): The male strip club Patti encounters in the game is called Chip N' Dale's, a parody of real-life male strip club Chippendale's. (Credit: SlyDante)
Status: Unverified

TV Shows (Looney Tunes): If Patti dies at the hands of a feral pig, the little "Game Over"-style screen has an animation of a feral pig bursting out of a Looney Tunes-style logo, just like cartoon character Porky Pig when he announces, "That's all, folks!" (Credit: SlyDante)
Status: Unverified

Leisure Suit Larry 5: Passionate Patti Does a Little Undercover Work (PC)

Real Place (Hard Rock Cafe): The Hard Disk Cafe is a spin-off of the Hard Rock Cafe. (Credit: Andy Thorley)
Status: Unverified

Famous Person (Various): Throughout the course of the game, Patti has erotic dreams about three rich celebrities: Donald Trump, Bill Gates, and (I'm honestly not kidding here) Uncle Scrooge. Also, the casino in Atlantic City is called "Tramp Casino", an obvious reference to Donald Trump. The store in Atlantic City where you get your roller skates is called "Ivana Skates", and the clerk in the store bears a strong resemblence to Ivana Trump. (Credit: SlyDante)
Status: Unverified

Famous Person (Various): The basement in Baltimore's K-RAP studios contains statues of singers Barry Manilow and Connie Stevens, jokingly referred to as the king and queen of rock. The rappers found in K-RAP studios are called Contested Development and P.C. Hammer, obvious parodies of real-life rappers Arrested Development and M.C. Hammer. (Credit: SlyDante)
Status: Unverified

Famous Person (George Bush/Dan Quayle): After you successfully land the plane, President George Bush makes a phone call to congratulate you (he was the current president at the time of the game's release), and he invites you to a banquet featuring Vice-President Dan Quayle. (Credit: SlyDante)
Status: Unverified

Specific Reference: The entire plot of the game is an in-joke to the Leisure Suit Larry series. See, there was NO Leisure Suit Larry 4, and in this game, Larry suddenly has amnesia, and the game's villain, Mr. Big, has supposedly stolen "the missing floppies" for Leisure Suit Larry 4! (Credit: SlyDante)
Status: Unverified

Leisure Suit Larry 6: Shape Up or Slip Out! (PC)

Products (Various): Most of the women you have to, um, "conquer" in this game are named after fine wines: