Death's Face exclusive to the Genesis/MD version as the 4th side scrolling stage music. Resurfaces in Thunder Force AC/Thunder Spirits later as a replacement for one of two TFIII stages.
Tan Tan Ta Ta Ta Tan, the config screen music. This is actually something of a trademark theme for the series, first appearing in Thunder Force II (as the config music and in a slower variant for the loading screen in the X68k version. As opposed to the brief few seconds you hear it in the Genesis/MD version.) Then later being in TFV and VI.
The Broken Thunder Album introduces Steel of Destiny -Take Off-, the ultimate version of the song that incorporates live guitars. The result is amazing.
Duel of Top, the Stage 5 boss theme. Basically, an even more awesome remix of Lightning Strikes Again from TFIV. Very fitting considering what the boss is.
KIN3-COOL, the "A" alternate for ORN-Faust encounters. A remix of Cool's Theme from Segagaga.
KIN3-CERB, the "B" alternate for ORN-Faust encounters. A remix of His Behavior Inspired Us With Distrust from TFIII.
The Stage 5 boss features Orn Styx, Orn Rynex and Orn Gauntlet which are remixed versions of title themes from the 3 previous games (The Wind Blew All Day Long for Styx, Lightning Strikes Again for Rynex, and Beginning of War for Gauntlet), as you fight super-sized versions of the highlighted ships for those games.
Orn Emperor, the last boss theme. Part 1 and Part 2
Broken Thunder
The end product of this turned out unfortunate, but it features some music that was originally meant to be used in TFVI before it's Development Hell period. It is awesome:
The Justice Ray Part 3 Fun fact: after TFVI was initially canceled, it was used in the Simulation/RPG game Segagaga as the boss theme for the Thunder Force inspired side scrolling segment at the end of the game.