Here is a complete list of all references and private jokes that found their way into Heroes VI.
Legacy Heroes:
Lord Kilburn appeared in Might & Magic 1, Heroes 1 & 2, and was mentioned in M&M 6
Lord Haart appeared in Might & Magic 2 and Heroes 1, 2 & 3.
Maximus appeared in Might & Magic 3 and 7, and Heroes 1 & 2.
Adelaide appeared in Heroes 3 & 4.
Moander appeared in Heroes 3 & 4.
Luna appeared in Heroes 1, 2, 3 & 4.
Ludmilla appeared in Clash of Heroes.
Kaspar appeared in Heroes 5.
Nymus appeared in Heroes 3, and in the M&M novel “The Sea of Mist”. Her bio lampshade the existence of another (male) hero called Nymus in H5.
Lorhish appeared in Clash of Heroes and might turn into Grawl from H5. He is named after Capybara's composer Sean Lorhish.
Jeddite appeared in Heroes 3 & 4. His bio mentions he saw under Kha-Beleth's helmet, which mirrors his original bio which mentioned he saw the demon king Xenofex' true face.
Xana appeared in Dark Messiah.
Atlas appeared in Might & Magic 5 and Heroes 1 & 2.
Kalindra appeared in Might & Magic 5 and Heroes 2.
Ciele appeared in Heroes 3 (Armageddon’s Blade).
Tazar appeared in Heroes 3 & 4.
Shiva appeared in Heroes 3 & 4. Her bio mentions the Dragon Utopia (classic Heroes location), the Sunken Temple (from H5), the Tomb of a Thousand Terrors (final dungeon of Might & Magic 4 and 9) and the Thunderbird (Stronghold unit in Heroes 3 & 4).
Heroes:
The hero Mokka is named after a restaurant in Budapest where Ubi and BH teams had dinner a few times.
The hero Umberto is named after Umberto Eco. His character is similar to Eco's William de Baskerville from The Name of the Rose.
The heroes Igor and Gritchka (seen in Haven 2) are named after Igor and Grichka Bogdanoff.
The hero Erika is named after the late Erika Walters (a.k.a Flamestryke), who hosted one of the most complete websites dedicated to the M&M RPGs before she tragically passed away a few years ago.
The hero Harald is named after M&M fan Znork.
The hero Eduardo is named after M&M fan Vitirr.
Sir Jaywoods the vampire is a pun on James Woods (who appeared in the movie Vampires) and also the name of a place near Kurt McClung's hometown in Indiana.
Cordelia is named after the character Cordelia Chase from TV series Buffy and Angel.
Montbard the Red Templar is named after André de Montbard, one of the founders of the real-world Templars.
Ishtvan Griffin is named after Istvan Zsuffa, Black Hole's Creative Director.
Acamas is named after the Cyclops of the same name that appear in Greek mythology.
Zhaoyu is named after M&M fan EvilP (aka Moyue).
Other characters:
Azkaal is named after Askaal, an alias used by Loic Portnoe, a game designer who worked on various M&M projects. Early in development that demon was actually called Nar-Olosshtu...
Towns:
A necropolis town in the map Stronghold 3 is named Abin-Sur in reference to a comic-book character (one of the Green Lanterns).
A Haven town in Necropolis 1 is named Skarena. Skarena is the Breton name of Scrignac, the small village Julien Pirou's family comes from
Castle Portmeyron in Inferno 4 is named after Portmeyrion, the village of the TV series The Prisoner.
The town of Seahaven in Inferno 4 is named after the city of The Truman Show.
The town of Sorpigal-by-Sea bears a classic town name from the Might & Magic series (Sorpigal was the starting town of Might & Magic 1, and New Sorpigal was the starting town of Might & Magic 6)
Several towns are named after towns that appeared in previous Might & Magic games.
Most of Stronghold town names are real Maori words.
Many Inferno town names are based on demon names from the Ars Goetia (Lesser Key of Salomon).
Abilities:
The icon for the Taunt ability looks a lot like the "Rude Frenchman" from the movie Monty Python and the Holy Grail.
Artifacts:
Angelic Alliance was an artifact in Heroes III the Shadow of Death.
Sword of Whistlebone was an artifact in Might & Magic VIII.
Iron Feather was an artifact in Might & Magic VII.
Souldrinker is based on an unused concept art from Dark Messiah. A different Souldrinker sword appears in Dark Messiah as well, hence the reference to several cursed blades bearing the name.
The Staff of Sandro is obviously named after fan-favourite hero Sandro.
Many artifacts are based on classic artifacts from the Heroes series.
The Guardian Set is similar to the Battle Garb of Anduran, the very first artifact set that appeared in Heroes 2.
Crag Hack's helmet is a reference to fan-favourite barbarian hero Crag Hack.
Quests:
In Stronghold 4, there's a quest to find the wreck of the "Jolly Raven", a pirate ship sunken "25 years ago". Finding the wreck of the Jolly Raven was one of the quests of the original Might & Magic RPG 25 years ago.
In Inferno 2, a Quest is titled "Secret of the Inner Sanctum", the subtitle of the first Might & Magic game.
In Inferno 4, a Quest is named "Be Seeing You", another reference to The Prisoner...
Achievements:
Mandate of Heaven is a reference to Might & Magic 6: The Mandate of Heaven.
Solmyr's Student is a reference to fan-favourite hero Solmyr ibn wali Barad.
The Gathering Storm is a reference to the first add-on to Heroes 4.
Festival of Life is the name of a campaign in Heroes 3 Armageddon's Blade.
Follow Me If You Want to Live is a reference to a line from the Terminator movies.
Foolhardy Waywardness is the name of a campaign in Heroes 3 Armageddon's Blade.
For Blood and Honor is a reference to Might & Magic 7.
Day of the Destroyer is a reference to Might & Magic 8.
Disciple of Sheltem is a reference to Sheltem, the first Big Bad of the Might & Magic games who destroyed whole planets.
Ironfist is a reference to the Ironfist dynasty of Varn and Enroth.
Dwarven Treasury I, II & III are a reference to an adventure map location seen in Heroes 3.
Dragon Utopia is a classic adventure map location of the Heroes series.
Clunkfest is a reference to a comment made by M&M fan Dreamwright on the forums (about some units having such over-the-top armors it was becoming a "clunkfest").
In Yog's Footsteps is a reference to fan-favourite hero Yog, a former Wizard who rejected magic to become a barbarian.
Gryphonheart is a reference to the Gryphonheart dynasty of Erathia.
Back in Black is a reference to a song by AC/DC.
Terminator is NOT a reference to the movie of the same name but to an enemy seen in the old Might & Magic RPGs which could exterminate party characters.
Nobody is Left Behind is a reference to Disney's Lilo & Stitch. Really.
The Untouchables is a pun in reference to Eliott Ness and his crew.
Demolition Man is a reference to the Stallone/Snipes movie of the same name.
Requiem for a Dream is a reference to the movie of the same name.
The Pusher is a reference to a song by Steppenwolf, featured prominently is the movie Easy Rider.
Quick and Furious is a reference to the movie franchise The Fast and the Furious.
Misc:
Several classic items can be seen on the Hall of Raiders and Artifact Merchant buildings: Armageddon's Blade, the Lion Shield of Heroes II and Lord Kilburn's shield seen in Might & Magic VI.
In Necropolis 4, a signpost mentions a "Temple of Meow" dedicated to the worship of Rakshasas. It's an old joke in the M&M series where each Might & Magic world had its own "Temple of (animal sound)" (Temple of Bark, Temple of Baa, Temple of Honk, Temple of Moo, etc.)
In Necropolis 4, a signpost mentions Lord Kilburn's maps of the desert being the most accurate. In Might & Magic 1, the player needed to find Kilburn to obtain a map of the desert.
The underground city of Sarkomand and its "winged lions" (Lamasu) is a reference to a place seen in HP Lovecraft's Dreamlands (especially The Dream Quest of Unknown Kadath).
In Haven 3 a signpost is dedicated to Zedd, an M&M fan who passed away during the production of H6.
In Inferno 1, some signposts contain references to the movie Princess Bride.
Several references to fan-favourite Barbarian hero Crag Hack in signposts, and mentions of his feud with Baron Rufus. Rufus is the name of Varkas' dog in Clash of Heroes, so Varkas might be a descendant of Baron Rufus himself and named his dog after his famous ancestor.
Various references and (very probably bad) puns in Quest names.