(^that never happened^)
"The flow of time is always cruel... its speed seems different for each person, but no one can change it..."
We love the idea of messing with linear time in games because Sheik's words in Ocarina of Time are painfully true in real life. Plenty of games use time travel dynamics to solve conflict on different scales. Part of the reason Majora's Mask is so poignant may be because you manipulate time in part to deal with mundane problems: I think it's the closest thing to our lives and what we can't do about them.
But I've been fixated on the large scale - alternate histories - lately, maybe from watching Code Geass. Pulling off a good alternate history game involves very complex world building and stretching the limits of suspension of disbelief. When they work they can be amazing and terrifying. I believe part of what makes BioShock games so attractive, beyond philosophical themes and well, being fun, is that their versions of the past are some of the most well thought out and convincing around (that faux-educational video ad was brilliant).
Alternate history, whether fixing disasters of the past or exploring an unsettling world in which they weren't, is a genre I wish were more popular in gaming. There are opportunities for writers to really get zany with premise (within the bounds of being smart, of course). Do you guys have favorite alternate history games? Or better, what alternate world would you want to play around in? Toy with events leading up to WWI! Stop the St. Bartholomew's Day Massacre from happening! Ok, maybe not that last one.
Good, now everyone go watch Iron Sky.
Image from good ole Wiki