Great list and retrospective, though for me AYAOTD will always be my number one favorite Nick show ever. I remember watching Nick in 1992 and seeing the promos for it and as a long-time Horror fan at the young age of 5, I knew I had to watch it. The rest is history and my childhood 
That is one of my all time favorite Nick shows too. Some of those episodes were really well done and creepy on top of that. At the top of my head, some of my favorite episodes included:
The phantom that lived in a girl's room, who would later die in a fire.
The clown "Zippo" (sp?) that chased a kid in a Fun House
The episode where the girl enters a doll house and notices her friend is becoming a doll
The abandoned building that contained abducted children
The episode with the Deaf girl and the punk kid going into some outer space environment.
There is probably more, but I have to go back and rewatch the series again.