My favorite part of FoE was the argument between Readeye, Autumn Leaf and Pip in the cathedral up to the part where Pip explained she isn't the element of honesty.
In Pink Eyes I love the running gag of The Count, makes me smile.
MN7 is the bit right at the start with Merky desperately trying to finish the drawing of his mother as he's dragged off.
PH is tougher, so many great moments but Rampage is my favorite character from anything ever so I think finally learning who she is is my favorite part. That and the epilogue.
EDIT: Great, now I'm remembering all of the Maruders backgrounds... and BigMac's... and Twilight... P21... Glory... Daus... Psalm...
and I'd only recently stopped crying after reading PH. God I love that story!
Favorite Moments from the Fallout Equestria
Highlight if you want to see it. Or another one with Murky later in that same Chapter. "I slammed forty copies of Wingboner Magazine down on the table. "...Ten tins All yours." " Murky Chapter 9 page 952 
Once again Highlight 
Some roads are Straight and Narrow, Some paths are high and Steep. Some ways are slow and Heavy, some Tracks are dark and deep https://www.youtube.com/watch?v=ZQlEOx9-EM0
Life's like a box of chocolates! Except I'm more fond of cupcakes. 
