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.
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.
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.