I always liked the Rugrats Halloween episode. I guess just because the show is good, and I like the early look of it, especially in the darker (visually) episodes. It successfully captures the feeling of learning about Halloween. It hits that very early nostalgia. Earlier than other Halloween specials.
I never watched Scary Godmother until last year, despite being the right age and loving Mainframe, specifically searching out all their stuff until well after ReBoot was over. I can't believe I missed it when I was a kid. It's actually pretty funny. That skeleton who lives in the closet was pretty clever. Also, I just have always liked early CGI, especially Mainframe's style.
Halloween is Grinch Night is another underrated one, and I'm glad OP mentioned it. It's actually pretty scary, as far as stuff aimed at that age group goes. I'm a teacher and one time someone decided to turn on Halloween is Grinch Night for the kindergartners when it happened to be raining during recess near halloween. Lots of kids cried at that one part where the Grinch finally does his thing. I hardly blame them. Though other kids, the cool kids, thought it was awesome, and it's sad that the crying kids probably mean they won't show it for any other classes. It's a good lesson to suck it up and enjoy something that's cool. The cool kids should get to enjoy it.