Most Convoluted Timelines

So let's just lay it all out. A rabbit draws Donnie Darko away from his bed so he doesn't get killed by a jet engine from the future. From this point, Donnie has 28 days to save the world... by ensuring that the jet engine go into the past and actually kill him this time. When he succeeds, the guy who turns into the rabbit never actually turns into the rabbit and therefore could never have taken Donnie from his bedroom in the first place. So, unless the whole film is a dream, Donnie Darko's ultimate timeline would have been the same if it never even happened at all. That is the epitome of convoluted.

Honestly, almost every superhero comic in existence could make this list, but the DC Comics universe really takes the cake when it comes to convoluted timelines. Ignoring the fact that many of their characters have been active for more than fifty years (yet remain roughly the same age,) you have the creation of multiple universes to explain continuity errors, the destruction of said universes to streamline continuity, and the resurrection of said universes to fix what was broken with the streamline. As a result, the average DC Comics character has more origins than there are issues of The Goon, and, while often fun, it's more than a little hard to keep track of.

Stephen King's Dark Tower series may look like a mere Western from the outside, but it's anything but. Things start to get weird in the second book when King introduces doorways into different times of our world, which allow him to pluck teammates from one door while affecting their history with another. 

These time hops expand from our world to alternate worlds, and before long almost the entire Stephen King canon rests somewhere under the Dark Tower's umbrella. Not only that, but King's real-life brush with death becomes part of the story, too. It all reaches a crescendo of confusion before ending in a typically disappointing mess. For the first four or five books, though, it's a total blast.

That Futurama has a convoluted timeline kind of goes without saying since it's both a parody of science fiction tropes and an interesting science fiction show in its own right. In other words, the timeline is convoluted but often in the service of good comedy.

Not only is young Fry an ancestor of old Professor Farnsworth, but after going back in time and having sex with this grandma, he is his own grandfather as well. That's just the start of this show's time traveling hijinks, which are so fruitful that they can make a "go back in time to kill Hitler" gag go by so fast you almost miss it the first time. Each marker in this show's convoluted timeline is a joy.