You'll notice as this list goes on that I'm very fond of drama and climax in video games. And nothing is as dramatic or climactic as a good boss battle. This is why most of your classic RPGs have two (usually exactly two) non-Big Bad boss battle themes: one for the common bosses, and one for the handful of REAL bosses. (Chrono Trigger has three, but that's a bit of a special case; we'll get to that later.)
You'll also notice as this list goes on that I'm fond of music that has a good opening riff. This track qualifies on both those counts. It's used for five or six boss battles in Chrono Trigger: Masa&Mune (their individual forms Masa and Mune get the normal boss music,) Azala/Black Tyrano, Great Ozzie/Super Slash/Flea Plus, Rust Tyrano, Son of Sun, and Zeal (if Magus isn't in your party). The latter four are in the endgame, so really that leaves just the two bosses that the game declares, by giving them this music, to be the most important in the game (other than Magus).
This music's tone is unmistakable. The first time you hear it, when you encounter the Masa&Mune battle, you immediately realize: it is on. Cue big gulp. (Masa&Mune turns out to not be a particularly tough boss, but still. It's an important battle, is what you instantly realize.)
Then, near the end, in lieu of any textual development, the programmers just use this music to make the player understand that Son of Sun, who the player has never heard of before even once, is a serious boss and that the Sun Palace is not a plaything. And it works, because the music is just that good.