Narm Charm: Some of the children providing the voices were too young to understand their lines, resulting in the classic awkward delivery that later became a staple of all Peanuts specials (the lines you hear are often a composite patched together from several different takes).
The whole "Snoopy shot down behind enemy lines" sequence. That eerie flute music (coupled with the distant gunfire and air-raid siren) doesn't help.
Not to mention the opening title sequence, especially the Ominous Owl at the very end.
Completely justified, of course, since this is a Halloween Special we're talking about.
The Woobie: Charlie Brown, as always; Linus, when he is still freezing in the pumpkin patch at 4 a.m.
Probably the most extreme example for Charlie Brown. Apparently this child is even deeply hated by adults, so much so that they would all give him a rock as opposed to candy.
Schroeder plays some WWI songs for Snoopy. Snoopy dances to the music, but when Schroeder plays a couple of sad songs, poor Snoopy starts crying so hard that he leaves the party. It just makes you want to give Snoopy a hug.