Cosmic Valley Zone, by davee0
Custom textures all lend to a unique atmosphere, making this level stand out. The usage of blue lighting make it shine more, and the skybox is very animated and gorgeous.
Nova Shore Zone, by DrTapeworm
The usage of a custom palette to give off a unique vibe instantly propels this level to one of the more unique looking ones, but if that wasn't enough to sell you, then the fantastic repurposing of Asset Pack textures and the array of custom badniks will.
Scarlet Palace, by .Jazz.
This level maintains a strict color palette throughout, and this results in a map that looks breathtaking when compared to other levels. Even little touches such as remapped textures and enemies to fit this theme go a very long way.
Doomsday Disaster Zone, by Lat'
Lat' shows his talent for making custom special effects for this boss, and the impressive scrolling special-stage like skybox create a Doomsday-style fight that leaves an impact.