When Zack meets the little Cloud from this timeline:
Zack:' More importantly… Cloud, did you shrink?
Mini!Cloud: How do you know my name?
Zack: You're kidding. It is you? Did someone cast Mini? And then Confuse? Was it a marlboro? Those things are vicious.
In the penultimate chapter, Cloud and Sephiroth fight again, this time because of JENOVA's influence. Genesis brings an end to it by throwing Firagas at JENOVA. Repeatedly. Also, counts as his Moment of Awesome.
Genesis: "Honestly. I'm not sure what I missed, but it wasn't even a moving target."
The author later wrote a bonus story based off the epilogue.
This little tidbit on the crossover between TFA and The Fallacious Goddess.
Zack: "Wow Sephiroth, you’re a dick in all dimensions, aren’t you?"
Sephiroth: "Except this one, apparently."
Also from the same fic, the running gag of everyone who sees both Clouds asking the one from TFA.
"Cloud, how many times did you time travel?!"
Cloud, very reluctantly, agrees to crossdress once again in order to retrieve "dangerous merchandise" Don Corneo has somehow procured. After a lengthy and humiliating trip, Cloud finally retrieves the box where it is kept and checks it. He quits once again when he sees it's actually a collection of action figure prototypes featuring him and the other First Classes.
The main reason he agreed to do so, besides the fact he thought it was something dangerous, was seeing Zack's attempts at crossdressing.