Zak McKracken and the Alien Mindbenders (PC)

Cross-Series (Maniac Mansion): Both Maniac Mansion and Zak McKracken were made by LucasArts around the same time, and when you find the chainsaw in MM, your character notes that there's no chainsaw fuel for it, and there's none you can get in the game. In Zak, you find chainsaw fuel...but it's noted there's no chainsaw you can get in the game! Freaky, huh? (Credit: SlyDante)
Status: Unverified

Zanac (NES)

Cross-Series (Guardic): If you beat the game, press A & B on Controllers 1 & 2 after the fairy stops moving during the end credits. The message, "See you again in Guardic" will appear. Guardic is an MSX shooter also made by Compile.
Status: TRUE: Verified by FO.

Cross-Series (Guardic): The level 6 boss is made up of tiles that spell out "GUARDIC".
Status: TRUE: (Screenshot) proves it.

Programmers: In level 6, there are floor tiles that spell out "COMPILE", the name of the company that made Zanac.
Status: TRUE: (Screenshot) proves it.

Zero Divide (PS1)

Cross-Series (Phalanx): There is a hidden game called Tiny Phalanx. It is a 3 level game that plays just like Phalanx on the SNES, with original stages and even its own invincibility cheat. (Credit: Deathspork)
Status: Unverified

Zero Wing (Multiplatform)

Cross-Series (Truxton): The design of the ship you control (the infamous ZIG that you may remember from the "All Your Base" fad) seems to have been inspired (or directly taken) from Toaplan's earlier shooter Truxton. The very first enemy ships you encounter do look a lot like ZIGs. (Credit: Dire 51)
Status: TRUE: Screenshots prove it: (Truxton Pic) (Zero Wing Pic)

Music (Can-Can): The track "Dancing Raisins!" is the Can-Can. (Credit: Andy Thorley)
Status: Unverified

Zillion (SMS)

Cross-Series (Fantasy Zone): Opa-Opa from Fantasy Zone puts in an appearance here. (Credit: Dire 51)
Status: Unverified

Zoda's Revenge: StarTropics 2 (NES)

Cross-Series (Tetris): You collect tetrads, or Tetris pieces. (Credit: Deathspork)
Status: TRUE: Verified by FO. (Screenshot) proves it.

Famous Person (Various): As Mike travels through time, he meets many famous historical people, both real and fictitious, such as Leonardo da Vinci, Cleopatra, Sherlock Holmes, King Arthur, Merlin, and Lancelot. There is also a reference to Marco Polo.
Status: TRUE: Verified by FO. (Some of my screenshots are glitchy due to poor emulation. I apologize for that.)

Cross-Series (Super Mario Bros.): When you have to go get the pizza for Cleopatra, the guy with the pizza is riding a Koopa Troopa. (Credit: Codie Martin)
Status: TRUE: Verified by FO. (Screenshot) proves it.

Products (Little Caeser's/Pizza Hut): When you deliver the pizza to Cleopatra, notice the bottom of the box after she finishes the pizza: Caesar's Hut. Hmm... a cross between Little Caesar's and Pizza Hut perhaps, or just a tribute to Pizza Hut with a little Roman twist? You decide. (Credit: Mike Waters)
Status: TRUE: (Screenshot) proves it.

Famous Person (Picasso): The caveman artist, Pikazo, is obviously named after Picasso. (Credit: Flying Omelette & Anenomephobic)
Status: TRUE: (Screenshot) proves it.

Music (Surfin' Bird): The magic words used to invoke the Oxford Wonder World's time travel powers (Papa Oom Mow Mow) are taken from the Trashmen's song called "Surfin' Bird".
Status: TRUE: (Screenshot) proves it.

Mythology (Mesopotamian): In Castlevania 3, Dracula's final form is that of the Mesopotamian demon, Pazuzu. In Zoda's Revenge, Zoda-Y's second (and final) form is also a Pazuzu. Zoda-Y is the boss of the Transylvanian mansion level. Coincidence? Possibly. But a Pazuzu is still a mythological reference, regardless.
Status: TRUE: Verified by FO.

Famous Person (Various): In the Italy Chapter, there's a guy on the street selling maps to the artists' homes. He names off Donatello, Michelanago, Raphael, and then he says he's sold out of Leonardo maps. Yes, I know these were all actual artists, but they weren't the ONLY renaissance artists, and it's an awfully big coinkydink that he would just happen to mention only the ones the Teenage Mutant Ninja Turtles are named after.
Status: TRUE: Screenshots prove it: (Screenshot 1) (Screenshot 2) The screenshots are glitchy due to poor emulation, but the text is still readable.

Cross-Series (Tetris): Hirocon, as seen in the ending, bears a rather strong resemblance to Tetris creator Alexey Pazhitnov. (Credit: Andrew Rae)
Status: TRUE: Verified by FO.

Zone of the Enders: The Second Runner (PS2)

Cross-Series (Gradius): In Anubis: Zone of the Enders (AKA Zone of the Enders: The Second Runner), the Vic Viper (of Gradius fame) shows up in a cameo role as the mech used by Leo Stenbuck, the hero of the first ZOE game. It's playable in multiplayer as well as in a Gradius minigame called Zoradius. In addition, to unlock the Zoradius minigame, you have to start a battle against Vic Viper in EX mode, pause the game, and input the Konami code (UUDDLRLR...) (Credit: Dan Tanaree)
Status: Unverified