Toshiharu Yamanishi - Metal Squad - Thunder Force IV.
Masahiko Yoshimura - Honjin no Theme [Headquarters] - Shining Force.
Motoaki Takenouchi - Into the Darkness - Shining Force II.
Motoaki Takenouchi - Elven Town - Shining Force II.
Motoaki Takenouchi - Water Goddess Mitula - Shining Force II.
Hikichi, Iwadare, Kubotera, and Mizoguchi - Stage 1 (Asteroid Field) - Advanced Busterhawk - Gley Lancer.
Foltan, Gigor, and Fazekas - Two Tides - Ecco: The Tides of Time.
Foltan, Gigor, and Fazekas - Fin to Feather - Ecco: The Tides of Time.
Alexander Brandon - Space Battle 2 - Tyrian.
Junichi Nakatsuru - Eternal Struggle - Soulcalibur II
Bob Siebenberg - Intro (MT-32) - Space Quest III.
Dobos, Heger, Magyari, and Zuckermann - Flashback: Battle of Wolf 359 (Saratoga lavel) - Star Trek DS9: Crossroads of Time (Sega Genesis).
Donald Griffin - Arab Rock - Aladdin (Sega Genesis).
And they all skirt by on a technicality as they were all featured in these games on various virtual 'radio stations,' but......
Philip Oakley - Together in Electric Dreams - GTA: Vice City Stories (Flash FM).
Too Short - The Ghetto - GTA: San Andreas (Radio Los Santos).
Rod Stewart - Young Turks - GTA: San Andreas (K-DST).
Hall & Oates - Out of Touch - GTA: Vice City (Flash FM).
DM - Personal Jesus - GTA: San Andreas (Radio X).
Bryan Adams - Run to You - GTA: Vice City (Flash FM) .
Missing Persons - Destination Unknown - GTA: Vice City Stories (Flash FM).
Toto - Africa - GTA: Vice City (Emotion 98.3).
And that's only a few.
UPDATE: I got another song to add to this post: Geoff Knorr - Destroyer - Civilization: Beyond Earth.