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These Refuge spaces show up a lot in games where exploration and treasure finding are important mechanics. Wright may have found value in worlds such as those created for the Metroid Prime games, where Samus Aran fights her way through enclosed ruins and passages riddled with secrets. Environments like the Chozo Ruins feature large, sheltering cantilevers and heavy stone construction, adding the somberness of an abandoned city with its lived-in look.
Concept art from the Metroid Prime series even at times resembles drawings of Wright's, like this one of the "Broadacre City" by showing similar spatial concerns.
While these examples take Prospect and Refuge for their individual values, there are instances in games that create very exciting sequences of these spaces. One such example is the stealth environments found in the Metal Gear Solid series.
I would argue that MGS's levels are actually based upon the Refuge-Prospect-Secondary Refuge sequence, as the stealth gameplay requires you to move from hiding place to hiding place. This type of gameplay changes mundane environmental elements like corners and lockers into safe places differentiated from the Prospect areas of the level with guards and cameras.
Half-Life 2, on the other hand, features a rather inventive expression of the Refuge-Prospect-Secondary Refuge sequence in the beach areas of the game. In this level, the player must cross a long stretch of beach without alerting alien insects called Antlions.
These monsters can hear the player character walk across the sand so the player must therefore use their Gravity Gun to move debris into bridge-like configurations between rock surfaces that the Antlions cannot reach. While not covered, the safe nature of the rocks makes them the Refuge spaces while the sand is the Prospect.
Previously worthless throwaway props like metal plates and wooden pallets become the most valuable items in the game, similar to Snake's legendary cardboard box. These items become portable Refuges: they are weaker in function than the level geometry versions, but their valued is heightened nonetheless.
Prospects and Refuges can also describe the mechanics of enemy encounters in games. To use Metal Gear Solid as an example: standard enemies are often found in areas where stealth is encouraged and therefore feature large percentages of Refuge space. In this way, Snake can sneak up on his foes and take them down silently in what is "typical" method of progressing through the game (people who still go through with guns blazing notwithstanding.) On the other hand, most boss encounters in MGS do away with actual Refuges altogether and opt for a more face-to-face spatial layout with most refuges existing as cover from weapons (again, with specific stealth-heavy examples like MGS3's battles with The End or The Boss notwithstanding.)
Another series of games where the number of Refuges changes in battle situations are those in the previously discussed Mega Man series. As discussed, the boss rooms in these games are large Prospect zones. This spatial type is very conducive to the types of theatrical showdowns that boss fights embody. Likewise, fights with smaller enemies often take place in areas where Mega Man can leap from platform to platform, allowing players to find good vantage points to shoot from or places to hide from enemy fire, such as when facing down enemies like Sniper Joe.
Spaces are given for hiding against minor enemies like Sniper Joe in Mega Man games while boss characters feature much more open rooms.
Prospects and Refuges are very useful for level designers as well as the player. However, there are elements of even refuges that if taken too far can create uncomfortable situations for players. Like any spatial survival concept, however, these can also be of great use to the level designer who is well educated in their usage.