The Square Demo version is my absolute favorite version of Prelude. You only hear it on the menu screen for several of the PS1 era demos Square packaged with their games.
Tough call, since I like most of them (sans maybe X’s) and most of them are pretty much the same. As for one of the most overlooked, however, I’d like to point to XI’s
My favourite is probably the one from A Realm Reborn (and the character creation theme for all the expansions since). Although World of Wonder from FFXV is up there too, along with FFIX, and the VIIR one.
I love how it starts off fairly sombre, but as it progresses there's a distinct undertone of hope there, and then just around the 2 minute mark when it seems like it will loop back to the beginning, it transitions into something more upbeat and almost celebratory, before ending on a hopeful and peaceful tone. It really feels like it's charting the tumultuous journey of the original 1.0 game through to the hope of 2.0 - that this really was a new beginning. (And I say this as someone who had no investment in 1.0)
Also the Weight of the World - Prelude version which combines the Prelude with Weight of the Word from NieR: Automata is also /chefskiss