AdventureQuest Worlds itself is one huge mix of the three main AE games, AdventureQuest, Dragon Fable, and MechQuest. Heroes and villains from all three have been featured in the game, although arguably the most evil villain of all three gets killed off right in the beginning of the game.
Before that, DragonFable and AdventureQuest had a crossover mission.
Also, AdventureQuest and WarpForce are in the same period of time, but it began with a crossover from AdventureQuest.
Aliens Vs Predator. Unlike the films, this series is actually really good. The Atari Jaguar game and the two PC games are considered classics in the FPS genre.
Angry Birds Rio is one with the film, as the poachers capture the birds, who escape and set out to rescue Blu and Jewel. Subsequent levels are set in the movie's Rio de Janiero and have the birds targeting the marmosets instead of the usual pigs. Blu and Jewel are also available as ammunition in some levels.
The "Red's Mighty Feathers" episode in the original game is one with Bad Piggies, as Red tries to bust the pigs' various contraptions to keep them from making off with an egg.
Battletoads and Double Dragon: The Ultimate Team was one of the earliest intercompany video game crossovers, which was made possible by the fact that both series were published in America and Europe by Tradewest. The game itself is really a Battletoads game with Double Dragon characters as guest stars (some of which were misnamed).
Blockland has a ROBLOXian add-on that can make it be this
Capcom and Valve are coming together to have a crossover of sorts in each other's games. For Valve, they are bringing Rochelle, Coach, Ellis and Nick (the survivor characters) to Resident Evil 6 on the PC in Mercenaries mode. For Capcom, they are bringing the Lepotitsa, Napad and Ogroman as special infected counterparts to Valve's special infected for Left 4 Dead 2.
Way before that, thanks to players modding the game, you can have various characters from many other games be playable within Left 4 Dead and Left 4 Dead 2.
Cross Edge is this in and out, with characters from the Disgaea, Darkstalkers and Atelier franchises making playable appearances (some, like Marie from Atelier Marie, being shown to international audiences for the very first time).
While we're at it, the first official mod for Skyrim, after the long-awaited HD Texture Pack... was a collaborative effort between Valve and Bethesda, showing just where that adorable littleSpace Core wound up.
And one of the fans wrote a mod that adds a crashed SSV Normandy from Mass Effect.
Forza Motorsport 4 features the Top Gear (UK) test track, and Jeremy Clarkson will provide commentary on dozens of cars in the Autovista mode. All the Reasonably Priced Cars from the UK and US Top Gear will show up as well.
The Warthog from Halo will appear as an Easter Egg in the Autovista mode with Cortana (Jen Taylor) providing the commentary for it in the place of Clarkson. Unfortunately, it's not drivable.
The finale of Ghost Recon: Advanced Warfighter 2 has the Ghosts call in an air strike, and in HAWX, you get to play the mission from the jet fighters' point of view. A similar crossover occurs between Future Soldier and HAWX 2.
Half-Life and Portal were originally different universes altogether. (GLaDOS vaguely alludes to the events of Half-Life once in passing, but that was just an easter egg.) But then! In Portal 2 you can find the drydock for a ship called the Borealis, and Half-Life 2: Episode 2 ends with Gordon Freeman about to set off to find it.
The shared universe is not only an allusion in the first game - in several rooms the player can find projectors with slides explaining explicitly that Black Mesa is a (hated!) competitor of Aperture Science.
Jewelry Master Twinkle, an already-obscure Puzzle Game, is actually a crossover between the Tetris TGM-like game Jewelry Master and the even-more-obscure mahjong game Taikyoku Mahjong Net-De-Ron.
One game in its 3D spinoff Maximum Impact (Mainly MI:2) had Hanzo Hattori from Samurai Shodown and Fio Germi from Metal Slug as unlockable characters.
Metal Slug 6 and 7 featured Ralf Jones and Clark Still (originally from Ikari Warriors, but using their appearances from the KOF franchise) as playable characters, with fellow Team Ikari member Leona appearing as a DLC character in Metal Slug XX, a PSP re-release of Metal Slug 7.
Even the venerable Mario Kart series does this... although most of the characters are Marioverse stalwarts, Donkey Kong and Diddy Kong are their Donkey Kong Country incarnations. Being co-developed by Namco, the Mario Kart GP arcade games go further than the home console versions and include characters from Pac-Man.
In addition to some already present in the KOF series, Neo Geo Battle Coliseum also added characters from other SNK titles that the KOF series didn't add, as well as some ADK titles (due to SNK Playmore's purchase of ADK after it filed for bankruptcy).
Pop 'n Pop, an obscure puzzle game does this with both the gameplay and the characters. The gameplay is essentially Puzzle Bobble with a few elements from Space Invaders thrown in while the roster is made up of characters from various Taito arcade games.
The Rival Schools games have had a few crossovers with Capcom's more popular fighting game series Street Fighter; the most obvious was Sakura Kasugano, Ryu's Hero-Worshipper, being a playable character in the console versions of the game. There is also a character known as Ran Hibiki, whose name is almost exactly the same as that of Dan Hibiki. Just what her relationship to him is undetermined, assuming there is a relationship at all and it is not simply an homage.
Hinata also claims to be a student of "Masters-ryu Karate" in Nekketsu Seishun Nikki 2, which explains why some of her special moves have the same flame effect as Ken's Dragon Punch in Super Street Fighter II.
Also in Street Fighter, Cody, Guy, Rolento, and Sodom from Final Fight appear as playable characters in the Alpha series. The crossover between the two also carried over into the cartoon, which featured a retelling of Final Fight's storyline while adding Ryu and Ken.
The Sega Superstars series subverts this at first, as it is essentially a collection of games based on Sega properties, but the second game, Superstars Tennis has Sega characters all play tennis together, playing the trope straight. Then there was a third racing game, which was a lot better than expected.
Before that we had, Fighters Megamix, which included most of Sega's 3D characters in a fighting game.
A small one in the With Friends line between Stampede Run and Words With Friends; you can pick up letter tiles from Words as bonuses in Stampede Run. Get enough to spell out a word and you earn extra gems and XP.
While it makes sense since they are a part of the same cosmology, most of Bioware and Obsidian's D&D-based games have subtle crossovers. Most notably, Baldur's Gate II features artifacts from some of the characters of Planescape: Torment, and one of said characters is also mentioned by an NPC in Neverwinter Nights 2.