The Transcendence AU is my favorite. I'm even writing an AU version of that AU. Haha, an AU for an AU. 

I CHANGED MY MIND. This one, the Immortal Pines AU is the best.
Basically, Dipper and Mabel get killed biting Weirdmaggedon or around that time, and it isn't what Bill wanted.
So he basically gives his power to them.
That's why their eyes are like that.
Also, they have... Issues. For instance, in the still ongoing web comic done by TawnaDuncan on Tumblr, Dipper has literally--No, I wouldn't spoil it.
Now go read it.

I know very little about this AU, and have never found the original fanfic.
All I know is: ITS AWESOME.

Apocalypse falls AU...Its interesting.
I won't explain everything... But, apocalypse.
Dipper gets bird wings, Mabel earns some serious skills. She also ends up stabbing Dipper at one point, which is why he has that stab wound and bandage around his midsection.
Pretty cool.

Monster falls is also another one I'm fond of. The picture explains all.

The Bill Pines AU... I know nothing about. It has always interested me so much and I've never read anything.
I take it this is the one where Dipper and Mabel are the demons, shaped like their symbols, and Bill is the human.
Actually, I knew that, why am I asking?

Demonic Guardians AU.
Aaaaaahhhhhvchnsjskksnsbsksjsvsbhs.
I like this one. I think.

I literally just found out about this one. Never seen it before.

Dipper's face on the bottom left tho.

And look how cool Bill is.

Reunion Falls. I read a story long ago...

Now, there are a ton of others, I just listed a few because I'm lazy.

Comment some of the other ones you know!