It began in a November 12, 2013 thread titled "Wrong Opinions on the Internet." One nonny brought up an author "who flounced from Thor fandom after declaring him evil" and proceeded to quote one of that author's fics:
None of the Asgardians seemed to see anything wrong with referring to a fellow sentient being that way.
Thor glowed with pride. They all glowed with pride, except for Loki.

There was a reply: "This is cracking me up. I'm going to start ending all of my sentences with 'except for Loki.'" And then there was a reply to the reply:

"Thor got ice cream. They all got ice cream, except for Loki."
"Thor went to the zoo. They all went to the zoo, except for Loki."
"Thor took a vacation to Cabo. They all took a vacation to Cabo, except for Loki."
Poor Loki.


It even fits with The Avengers!
"Thor got shawarma. They all got shawarma, except for Loki." 


"They got buttplugs. They all got buttplugs, except for Loki."
"And we all shine on. Like the moon, and the stars, and the sun. And we all shine on, except for Loki." 

"Except [for] Loki" has since become a very popular running joke on FFA, even if a few people have needed explanations for its sudden popularity.

Two of the best instances:

Fic Recs - Steve Rogers sucking cock

Anyone's cock but Loki's.

Steve Rogers sucked Thor's cock. He sucked Coulson's cock. He sucked everyone's cock. Except Loki's.
Now, Loki had had his cock sucked by a great variety of persons and creatures, some of whom had been quite talented. But there was something about Steve Rogers’ mouth, and also perhaps about the knowledge that that mouth had so recently been wrapped around his brother's cock, that made Loki want to experience it for himself.

In a subsequent thread, there was a comment about a horrendous disability issuefic featuring Tom Hiddleston as a double amputee. The fic featured this line:

“Tom.” The paramedic said softly their eyes meeting briefly. “You don’t have any legs.”

A truly awful hilarious nonny replied, "They all had legs. Except for Loki."

At least two FFA post headers have referenced the joke, FFA Post # 269, and FFA Post # 314, in which a confused, drunk (possibly enchanted) Thor keeps asking FFA to "accept Loki."