I’m going to give Tomoyo After, Kud Wafter, and the VN’s After Story a try before I vote here. I want to have all the choices available to me with this one.
That being said, out of the ones I have read, Refrain and AIR are some of my favorite story arcs from any Key game. It’s hard to choose between the two. For now, I’ll give a slight edge to Refrain because it gives you the choice for a happy ending or a more ‘realistic’ ending.