Everyone Is Jesus in Purgatory: It's possible to interpret every single timeline as how each member influences the group or what their personality is like. When Abed leaves the room, the group gets overwhelmed by their emotions. When Jeff and Pierce leave the room, the group became more cheerful and united.
Soooo, Troy keeps the chaos away?
Troy's the only one (possibly because he's just too dimwitted) of the group that is genuinely nice to everyone. He gets angry/frustrated like any person, but he has no prejudice. Think about it: In the first episode: Pierce hates young people (or all people, or life, or something...), Shirley's ultra-religious, Abed can only see people as tropes which inevitably leads to prejudice, Annie is a little pretentious/thinks she's smarter than all the others, Jeff definitely thinks he's too good for community college and Britta has her high-and-mighty 'look I'm an activist and I care about issues' thing going on.
Harsher in Hindsight: Troy's absence leading to the darkest timeline seems harsher after Donald Glover left the show in the fifth season, which became the last season after NBC cancelled the show. You could say Troy leaving the group really did lead to the darkest timeline. This was later subverted when it was announced that Yahoo! Screen would produce at least one more season with virtually the same budget as the NBC seasons.
Jeff, for using a six-sided die in a group of seven people to determine who has to go get pizza, meaning he'll never have to go to get pizza. Abed calls him out on it in the real timeline.
Abed also may count as this, seeing as how he sent a fake club invitation to Jeff a month ahead, just so he would keep his calendar open for the party.
Memetic Mutation: The moment where an oblivious, smiling Troy comes back to find the apartment is now a flaming warzone. It's since become one of the most popular reaction gifs on tumblr, particularly for when fandom arguments start exploding.