If you're willing to count individual pieces of equipment as well as abilities, FFIX crushes any other that I'm aware of. After disc four, a good deal of areas become blocked off, shops change, and, subsequently, multiple pieces of earlier equipment are no longer available. If the player forgets to purchase certain pieces ahead of time, he loses the opportunity to learn a great deal of the characters' abilities. What's more, if the player sells certain pieces of equipment after finding a better replacement (as I'm sure many are apt to do), some of the best equipment in the game can't be synthesized because the ingredients are no longer available.

Anyway, if one counts each piece of equipment and everything that becomes unobtainable due to its absence as a single lost forever, then I'm saying it goes to FFIX hands down.