The boards included in the Custom Board Medley are as follows. Easy, Normal, Hard, and Lunatic represent difficulty levels for the same board existing in multiple states. Easy is the simplest, and Lunatic is the most difficult. Board states marked with * combine features from multiple boards into a single board. Board states marked with , use doors to divide the board, with two boards constituting one board state.

• Enne-san Board 01
• Aegis Rim
• Enne-san Board 10 -Easy-
• Funky Stadium
• Enne-san Board 17 * Enne-san Board 42
• Hibiscus Mandala
• The Kanto Region
• Facing Worlds
• Enne-san Board 39 * Tetris FS
• Birdo's Big Top
• Bowser's Galaxy Reactor
• Enne-san Board 22
• Gal Da Val Island (Board State 1 and 2), King of the Hill (Board State 1) -Normal-
• High-Rise
• Planet Mira -Normal-
• Enne-san Board 15
• Fillmore
• The Clock Tower
• Yoshi -Normal-
• Goddess Crest
• Enne-san Board 18, Toads House
• King Boo's Haunted Hideaway (Board State 10)
• Yoshi Cloud * Venn Diagram
• Enne-san Board 48 * Enne-san Board 49
• Cogito Ergo Sum
• Castle Town
• Suits Map (Board State 1)
• Star Carnival -Hard-
• Luigi's Mansion (Board State 4)
• Enne-san Board 29
• Quadrants (Board State 1)
• Yevon * Enne-san Board 33
• Squid
• Enne-san Board 20 (Board State 10)
• The Palamecia
• Super Bowser's Trackway
• Enne-san Board 12 (Board State 1)
• Mirage Oasis * Enne-san Board 06
• Shibuya Underground
• Return to Lighthouse Island
• Gal Da Val Island (Board State 3 and 2), King of the Hill (Board State 2) -Lunatic-
• Planet Mira -Lunatic-
• Enne-san Board 52 -Lunatic-
• Colony 9
• Disboard (Board State 1)
• Playground, Enne-san Board 30
• Star Carnival -Lunatic-
• New Los Angeles
• Yoshi -Lunatic-
• Rainbow Road MKWii
• Enne-san Board 10 -Lunatic-