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
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 uses the emphasis bits to tint the screen green during gameplay (as the PAL console flips the red and green emphasis bits), but does not dim the screen when paused.

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

Cliffhanger
Cybernoid - The Fighting Machine on the top part of the difficulty select and better luck next time screens. Also uses red emphasis when the screen changes in-game.
Dragon's Lair
Felix the Cat
Fun House for fading out
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
Legend of Prince Valiant, The (E) uses full emphasis on the title screen, green emphasis for gameplay and red emphasis for status bar
Lethal Weapon
The Lion King (E)
Magician
Mickey's Adventures in Numberland
Muppet Adventure: Chaos at the Carnival
Noah's Ark (E) uses blue emphasis combined with grayscale mode to put part of the level underwater and all 3 emphasis bits in other cases
Qix
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
Space Shuttle Project
Super Spy Hunter, when paused. The Japanese version Battle Formula doesn't do this.
Xiao Ma Li

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.
Super Bat Puncher Demo dims the screen during pause.
Battle Kid and Battle Kid 2 dim the screen during pause.
Waddles the Duck dims the screen when on a warp, and RG-emphasis when in ice-dimension, among others.

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.