Great list! Love when unexpected guests join. President Wilson from Metal Wolf Chaos(A mecha game) joins Enchanted Arms(JRPG) as a playable character. Although afaik he's only available in the Xbox 360 version. Not the PS3 version. Both games are made from Formsoftware. But I think it fits he criteria for this list.

Yooka and Laylee show up in Demon Turf
Peppino and Clive (From Clive n' Wrench) show up in Antonball Deluxe
Sega All-Stars Racing Transformed has a ton of characters from other series
You can play as Aurora from Child of Light in Bloodstained: Ritual of the Night
A few different characters are DLC for Blaster Master Zero 2
Dead Cells had the "Everyone is here" Crossover
River City Ransom: Underground has characters such as the Castle Crashers and the main character of Hyper Light Drifter that show up in the background
Donkey Kong shows up in Punch-Out!! for Wii
Toree shows up in Lunistice

That's all I got for now.

Probably cheating but this is like the central gimmick for Dead Cells’s DLC. Great list as always!

Bloodstained's Miriam cameos in Blasphemous
Monster Hunter World has crossover boss battles with Final Fantasy's Behemoth and The Witcher 3's Leshen, and had Moogles and Geralt for the respective crossovers.
Shin Megami Tensei III: Nocturne is literally the origin of "Featuring Dante from the Devil May Cry series".
The Wonderful 101 has Bayonetta, Jeanne, and Rodin as secret characters from the Bayonetta series.
Speaking of, Bayonetta 2 on the Switch has nods and allusions to a lot of Nintendo properties, the most blatant one being the Chain Chomp which is an unlockable weapon (but its an actual, living Chain Chomp)
Crash Twinsanity has a very sudden and random Spyro cameo in the middle of one of its custscenes
The Wii U version of Scribblenauts Unlimited allows you to summon a ton of different Nintendo characters like Mario, Peach, Bowser, Link, Zelda, Ganondorf, among others from those two series.
Donkey Kong Country II has Link and Mario appearing in the final results screen.

All I got for the time being, hopefully this list won't be too much work to maintain.

Oh and Super Meat Boy. Waaaaay too many characters to list. You got representation from Spelunky, Minecraft, Braid, VVVVVV, Mighty Jill Off, I Wanna Be The Guy (*Internal Screaming), Half-Life, Bit.Trip Runner, Castle Crashers, and so on.

Mortal Kombat has Freddy and Bubba in it right? And a bunch of other weird movie people

gon (from gon) in tekken 3

Klonoa in Alpine Racer 3
Jack Frost in SBK Snowboard Kids
Jill (from Va-11 Hall-A) in YIIK

Sonic's an NPC in crusader of centy

The incredibly raw inclusion of Final fantasy/Dragon Quest characters to ball in Mario Sports Mix (and hoops 3 on 3 i think)

In Crash Twinsanity, Spyro is in a cutscene near the end of the game.

My bad, @AlphaOne2 beat me to it!

Hey everyone, I apologize for the late response! It was pretty late over here and so I went to bef shortly after making the list, but now it's time to add all.the suggestions!

@Detectivefail It does fit perfectly! To the list it goes, thank you so much!

@DeltaWDunn These are quite a lot, and all fit the list with no problems! Thank you so much for all of these! I don't know how I forgot about DK in Punch-Out, I love that one.

@cowboyjosh Delta beat you with that suggestion, but thank you nonetheless! And happy to hear you and the others like the list! Thank you for the kind words! :D

@AlphaOne2 Thank you so much for all these, they are all fantastic entries and I'll add them in a moment! And don't worry, mantaining these os easy, the only thing now is that I have to add quite a lot of entries because of my sleep schedule XD. Still, thank you so much! :)

@moschidae True! There are a few guests in some MK games, I'll check it and add the games, thank you!

@taigamask Ah, how could I forget the punching big head dino... I'll add it in a moment, thank you!

@MobileSpider I'll add all there in a moment, thank you so much for these suggestions! :)

@MagneticBurn Noted and will be added in a second! Thank you so much!

@Baird The surprise guests that confused kids across the world... I'll add the games un a moment, thank you so much!

@T0M196 Still, thank you nonetheless!

I had no idea who Starfy was when I played Super Princess Peach as a kid x)

@Dalaamclouds Added! Thank you so much for the suggestion, I had no idea Starfy appeared in that one!

Assassin's Creed Origins has a crossover with Final Fantasy XV with Ardyn and Bahamut appearing out of nowhere and it's super confusing. Similarly, I think there was an AC-themed event at one point in FFXV, though I don't know if any AC characters appeared there.

@Penumbra Someone actually suggested that one over on the discord server and I added it! Still, thank you for suggesting it and also talking about the FFXV event, I had no idea there was also one in that Game and it's super interesting.

All current games on the list finally have a description of the cameo in question! It took a while, and I apologise for the wait, but it's finally done! Now, to add even MORE entries!

A few more:

River City Girls features multiple characters from Double Dragon
Mario is the ref in Punch-Out!!
Mario and Peach show up in NBA Street V3 for some reason
The general in Tonic Trouble also makes a brief appearance in Rayman 2
Spider-Man is a boss in The Revenge of Shinobi
Starfox characters show up in Starlink: Battle for Atlas
Mad Scienstein from The Frog for whom the Bell Tolls shows up in Dr. Mario 64, Wario Land 3, and Wario Land 4.

@DeltaWDun I mentioned Mario being the referee in Punch Out in the Tennis NES entry and NBA Street V3 is already on here, the rest tho are fantastic entries and I have added all! Thank you so much! :DDDDD

Valkyria Chronicles had Vyse, Fina and Aika from Skies of Arcadia in as playable troops / Support.

@FallenGrace Added! Thank you! :D

Tekken 7 has Negan from The Walking Dead as a playable character (and also Akuma from Street Fighter, Fatal Fury's Geese Howard and Noctis from FFXV)

@Yanser94 I'll add it right away, thank you so much!

Lars Alexandersson from Tekken 6 is a playable character in Naruto Shippuden: Ultimate Ninja Storm 2

@cappone_ceraio Now that's one I didn't see coming... I'll add it right away, thank you so much!

There is a mini game in Metal Gear Solid 3 (Snake Eater and Subsistence versions) called Snake Vs Monkey. As Snake you try to stun/capture the monkeys from Ape Escape. Sadly, this was removed from the HD versions. :\

@Corrugated_Fox The fact that each major instalment of the series references each other is amazing, and it is a huge bummer that they took that part out from modern versions, that sounds hilarious and extremely cool. To the list it goes, thank you so much!

Chicory: A Colorful Tale - cameo by the Frog Detective
Haiku, the Robot - easter egg room with the Knight from Hollow Knight
Spelunky HD - Spelunky in Super Meat Boy has been mentioned, but Meat Boy is also a playable character in Spelunky

very fun list to read through, thank you

@Taaroni No, thank you for this suggestions, I'll add them all right away!

But really, thank you so much for reading and for the kind words! :D