Colour-emphasis games

The following is a list of games which make use of PPU register $2001's colour emphasis bits (D7 to D5):

Commercial

Bubble Bobble for the Famicom Disk System uses red emphasis to tint the screen throughout the game, which is absent in the cartridge releases.
The Fantastic Adventures of Dizzy uses it in the beginning when the scroll is unfurled.
Final Fantasy and Final Fantasy II rapidly sets and clears all 3 emphasis bits to flash the screen when going into a battle screen
Noah's Ark (E) uses blue emphasis combined with grayscale mode to put part of the level underwater.
Super Game's Aladdin uses red emphasis to tint the screen during gameplay, and all 3 emphasis bits to dim when paused. The official version of Aladdin, released only in Europe, also supports red emphasis to tint the screen during gameplay, but does not dim the screen when paused.

The following games set all 3 emphasis bits at once to dim the screen:

Felix the Cat
The Immortal
Indiana Jones and the Last Crusade (Taito), story scenes and some action scenes.
James Bond Jr
The Jungle Book
Just Breed
Lagrange Point uses colour emphasis, in some frames combined with grayscale bit to do a very cheap fade-out effect when switching to and from the menu on the playfield, and also when entering into battle
The Lion King (E)
Magician
Mickey's Adventures in Numberland
Rampart uses color emphasis on the player select screen, the options screen and some of the scrolling text. Blue emphasis is used for the score tally bar.
R.B.I. Baseball 3
Super Spy Hunter, when paused. The Japanese version Battle Formula doesn't do this.
Lethal Weapon
Dragon's Lair
Cybernoid - The Fighting Machine before game starts

Wall by Chris Covell uses a blue emphasis to simulate the water flooding the wall.
Graphics editor by Damian Yerrick allows applying a SCREEN TINT to the picture.
Munchie Attack by Memblers dims the screen upon Game Over.

Rockman 4 Minus Infinity (during Brightman's stage) darkens areas farther away from Mega Man.
Bisqwit's Castlevania II retranslation uses the de-emphasis bits to highlight a section of a screen when scrolling the list of savegame slots.