That is an interesting list
Top 5 favorite episodes:
#5 For the Triumph of Evil
The Sandman episode, being one of my favorite episodes due to one of the first signs of true trust towards the witnesses (Abbie and Ichabod). A choice to either lose Abbie, a woman he has only known for a short time or to possibly sacrifice himself in order to save her, it was one of their biggest moments.
#4 The Sin Eater
The Introduction of John Noble, (Was one of my favorite characters, and wish they just stuck with him as the Sin Eater) The episode itself was deep and changing in both character development and story arc.
#3 Mama
The reason why we need more Abbie backstory episodes. This had a huge impacted on who Abbie is and why. Mama didn't have everyone involved in the episode and still was one of those episodes you can't forget. The storyline, and character development was enough to capture the viewers and remain with them.
#2 Weeping Lady
I was about to place this as my number 1 episode since I've used it a couple times already, but it remains my second favorite. Either way it's an episode that reveals a different side to the characters, plus the fact of how the Weeping Lady was connected to Ichabod's past was a dark twist that I quite enjoyed.
#1 Pilot
Why is this my favorite because it's what started it all. The most well-written episode to where I can only think of one character I didn't care for but everyone else was just -- I couldn't wait to get to know these characters. And that just says allot.