Yeah RPGs have usually by far the best soundtracks of any games. I agree with moozooh that Chrono Trigger and FF6/3(US) have very good, if not the best soundtracks overall.
From top of my mind, my single favourites are:
- Chrono Trigger - Too Far Away Times (probably best)
- Chrono Trigger - Forest Theme
- Chrono Trigger - Ocean Palace
- Chrono Trigger - Epilogue
- Chrono Trigger - Magus Theme
- Chrono Trigger - Belthasar Theme
- Chrono Trigger - 1000 AD Theme (both, Towns and Field)
- Chrono Trigger - Schala Theme
- Terranigma - Underworld Theme
- Terranigma - Sea Port Theme
- Terranigma - Grecliff
- Terranigma - Elles Theme
- Terranigma - Crysta
- FF6 - Phantom Forest
- FF6 - Terras Theme
- FF6 - Celes Theme
- FF6 - Espers Theme
- Secret Of Evermore - Hall Of Collosia (First/Main Part)
- Secret Of Evermore - Puppet Show
- Secret Of Evermore - Ending/Credits Theme
- Secret Of Evermore - Queen Bluegarden Theme
- Secret Of Evermore - Lonely Ebon Keep Theme
- Secret Of Mana - Dark Continent
- Secret Of Mana - Sorrow Theme
- Secret Of Mana - Mana Field
- Secret Of Mana - Flammies Theme
- Seiken Densetsu 3 - Innocent Theme
- Seiken Densetsu 3 - Sacrifice Part 3