That's... kind of an odd question. Would you ask this about stories in any other medium? I found the film AMOUR about as much fun as doing my taxes, but I can see why some people enjoyed and cherished it.
I mean, for some of these games on your list, "fun" isn't even a factor in their design. Proteus has no objectives and contains no actual "game" -- it's simply an experience. Same with Dear Esther. Howling Dogs is essentially a short story which you read on a screen.
And some of these games are more directly disturbing -- some might say deliberately "un-fun". Cart Life is about forcing the player to experience poverty. Little Inferno cleverly and cynically skewers the entire idea of fun in games. Spec Ops is a brutal, horrifying, anti-war story inspired by APOCALYPSE NOW. To The Moon might make you cry.
In conclusion, play Hotline Miami.
Of course I'd ask. If I read a list of avante-garde movies, I might ask which are also entertaining. ANNIE HALL and ALL THAT JAZZ do interesting things with narrative. So does Memento. So does, if I remember correctly, SYMPATHY FOR THE DEVIL. I enjoyed three of them, and one was a slog.
You asked which ones were "fun", not which ones were "entertaining".
Anyway, if you're asking which of these games you'll enjoy... isn't that just personal preference? But if you really liked Papa y Yo, I'll take a wild stab and say you'll probably like Fez, Journey and Kentucky Route Zero.
Games that are actually game-y:
Hotline Miami (frenetic 2d murder rampage)
Spec Ops (Apoc Now in postapoc Dubai)
Fez (puzzle-y platformer)
Antichamber (Portal but ten times weirder)
Galatea (talk to a statue that has a baobab for a dialogue tree)
The Gostak (distim the doshes by flurbing the gostak)
First Draft of the Revolution
Walk through levels and experience stuff happen around you:
Proteus - boring as fuck, IMO
Thirty Flights of Loving
The Stanley Parable
Journey - needs to be played on an online PS3 for proper experience
Adventure-y storysome games:
To The Moon
Kentucky Route Zero
Swords & Sworcery
In conclusion, I blame Joss Whedon for ruining me and my ability to not adverb every noun I can get my hands on.
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