I am probably revealing a significant demographic disparity between myself and many of the active users of this site, but visiting real life locations within video games is a combination of my two favourite hobbies. A great travel memory of mine was visiting Venice shortly after playing Assassin's Creed II, set in Renaissance Italy, and recognising St Mark's Cathedral and the Doge's Palace from the game. As there are connections for WHS appearing in various film or book series, I thought it might be interesting to have a connection for WHS appearing within video games.
I would suggest only including examples of 'realistic' portrayals of WHS, in the sense that the locations are recognisable with some attempt at authentic portrayal. This excludes both examples of games naming unrepresentative locations after WHS (such as Iwami Ginzan Silver Mine being a generic cave level in Nioh) as well as fictionalised locations inspired by real places (like Unnamed Obviously-Kathmandu City in Uncharted 2). This leaves some degree of ambiguity, but seems better than a torrent of vaguely-European settings being listed as representing Rome, for example. I would also limit it to commercially released products, rather than free browser games or similar. Again, this leaves potential ambiguity. Basically, I am thinking of examples where the player can visit a reasonably accurate or representative depiction of a WHS, rather than just using it as a cursory background or something.
This category, unsurprisingly, is dominated by the Assassin's Creed franchise, which is the only game series I can think of that explicitly covets this form of 'virtual historical tourism'. If people think this is a worthwhile connection, I've come up with a list from things that I have played. I tried to mention specific individual elements of the WHS where possible. There are probably more from the realistic driving sim genre, at least.
Jerusalem – Assassin's Creed – Dome of the Rock, Al Aqsa Mosque, Church of the Holy Sepulchre
Acre – Assassin's Creed – Hospitaller Fortress
Damascus – Assassin's Creed - Ummayad Mosque
Florence – Assassin's Creed II – Duomo, Ponte Vecchio
Venice – Assassin's Creed II – St Mark's Cathedral, St Mark's Square
Vatican City – Assassin's Creed II – Sistine Chapel
San Gimignano – Assassin's Creed II
Rome – Assassin's Creed Brotherhood – Colosseum, Castel Santangelo
Istanbul – Assassin's Creed Revelations – Haghia Sophia, Topkapi Palace
Paris – Assassin's Creed Unity – Notre Dame Cathedral
Versailles – Assassin's Creed Unity
Routes of Santiago de Compostela – Assassin's Creed Unity – Tour St Jacques (with historical church still attached)
Palace of Westminster – Assassin's Creed Syndicate – Parliament, Westminster Abbey
Tower of London – Assassin's Creed Syndicate
Old Havana – Assassin's Creed IV – Castillo de San Salvador de la Punta, Havana Cathedral
Itsukushima Shrine – Nioh
Islamic Cairo – Serious Sam 3 – Mosque of Ibn Tulun
Memphis – Serious Sam 3 – Sphinx, Giza Pyramids
Assassin's Creed Origins – Sphinz, Giza, Bent Pyramid
Nubian Monuments – Serious Sam 3 – Abu Simbel, Philae
Thebes – Serious Sam HD – Temple of Hatshepsut