Thanks to this Dungeons and Dragons cartoon fan site they linked to, I now know the name of the episode that terrified the crap out of me as a kid - City at the Edge of Midnight. It began with a little boy getting up in the middle of the night. When he stepped out of bed, the floor started glowing and sucked him underneath and into the alternate world. His dad heard him yelling and tried to help, but to no avail. For quite a while after watching that, I was paranoid of stepping within about two feet of my bed, so I'd take flying leaps in and out. I can't remember when or why I quit doing that, nor can I recall anything else about that episode other than the kids being enslaved and forced to push some giant cogs around.
Of course, if I watched the cartoon now, I'd probably laugh my ass off at the cheesiness of it all. It's amazing what can scare you when you're five years old, though.