There are a fair amount in the Underworld and a... decent amount in the Overworld.
NPC 40 Dark Knight Cecil (You can use NPC 1 instead, don't forget to make him Visible though)
NPC 70 Paladin Cecil (To my knowledge is unused completely)
NPC 125 Unused Captain
NPC 127 Unused Chocobo
(NOTE: Old Man 147 "Not Used" is actually the Seneschal in the Tower of Babil.)
NPC 151 Unused Soldier (He is Technically used, but is quickly made invisible starting events. He would have stood, along with his clone in front of Eblan's Hospital)
NPC 166 Unused Mist Bomb (likely part of an earlier plan when they didn't have the Visual Effect prepared yet)
NPC 256 Dark Knight Cecil (Unused and placeholder.)
There may be a couple more in the Overworld, but those are the ones that should be safe.
Underworld
NPC 257 Dark Knight Cecil (Has no purpose in the Underworld)
NPC 303 Edge (A copy of Edge, you could replace with his initial entry at 276)
NPC 365 Grimoire Event 1
NPC 366 Grimoire Event 2 (NOTE: Since you are trying to recreate the game back to its original state. These events are in the original game, but so hidden away that I've only seen it mentioned in a couple of places. You can acquire the two Grimoires from the bookshelves in the Feymarch Weapon/Armor Shops after going to the Moon, I believe is the trigger)
359-376 (Training House NPCs 1?)
378-379 (Training House NPCs 2?)
380-387 (Programmer Room NPC leftovers?)
402 Obtaining Grimoire 91 (Unused completely)
411 Rosa (Likely used in the Lunar Whale, but they copy all of the NPC's there for some reason when they all had applicable Sprites before, making these a duplicate)
412 Adult Rydia
413 Edge
414 Kain
488 Tellah (Is never seen in the Underworld, making this unused)
492-494 (Training House NPC's)
NPC 495-510 are completely unused.
And that should do it! That should give you a little more room. A lot of room in the Underworld though. At least a new town or several new dungeons worth of NPC's available.