0180-0181:
Grunts by Zack for when Ifrit attacks him. However in my ears these grunts in the audio files don't match those used in-game. Due to the loud volume of the battle music and the sound effects in this scene, it is difficult to be sure. File 0182 is the sound of Sephiroth saying "hmph" before slicing down Ifrit, but you have to listen real carefully to hear this in-game.
0513 &
0514:
For when Zack jumps up from the floor in this church. File 0513 has both the sound of Zack's grunt and Aerith's exclamation, while 0514 only has Zack's grunting. It seems likely that 0514 is not used, though the sound is exactly the same as the one in 0513, minus Aerith's exclamation.
*
0712 &
0713:
Grunts by Angeal and Hollander when Angeal pushes away Hollander. The two files are very similar, but only one is used. I don't know which. This may be the only case of an unused voice file that is not identical to the one that is used. But the difference is so small that it's barely noteworthy. =/
0883 (and around those parts) :
In the final game, when you decide to leave Midgar for Nibelheim, you first get the scene with Zack and Cloud meeting, then immediately followed by the scene where Sephiroth reveals where they are going. Oddly enough, in the audio files, the scene between Tseng and Zack in the Sector 6 playground is placed inbetween the above two scenes.
Nothing special aside from that, it's just very rare for the audio file order not to match with the final game.
1051,
1052 &
1053:
Voices when Sephiroth sword-pushes Cloud into the Jenova chamber. 1051 has Sephiroth's sound, 1052 has Cloud's and 1053 has a mix of both. Listening to the in-game scene, the timing matches with 1053 really well.
1086 (and around those numbers) :
Unexpected order of Cissnei sounds. Her battle grunts from throwing the giant shuriken are placed *before* her line "If you want to escape, you'll have to..."
Again, mentioned only because in all other cases the order of the audio files match up with the script progression in the final game.
1100:
Cissnei: "He... He's the other sample they collected at Nibelheim.
Zack: "Why did you come here? I told you to go away."
1101:
Zack: "Why did you come here?"
1102:
Zack: "I told you to go away."
It would be most intuitive if 1100 is the one that's used.
1110:
Cissnei: "Tseng, I've lost the target." *Zack exclamation*
1111:
Cissnei: "Tseng, I've lost the target."
1112:
*Zack exclamation*
I can't tell if 1110 is used, or 1111 + 1112.
1142:
Cissnei: "Behind you" *Zack startled*
1143:
Cissnei: "Behind you"
1145:
*Zack startled*
I don't know if 1142 is used or 1143 + 1145.
1144 is Cissnei saying "So predictable".
Files
1294 -> 1348 are not playable. PotPlayer claims that these require a different audio decoder. These files are definitely not empty and are in fact way bigger than the normal 1-9 second clips.
1349, the last file, is playable. 61 seconds long it consists only of wind sounds. Probably used for the area of Zack's last stand.