I'm not sure if this is a comprehensive list, but:
  • Relic weapons (previously completed stages only)
  • Anima weapons (previously completed stages only)
  • Binding Coil of Bahamut armor and weapons
  • Second Coil of Bahamut armor and weapons
  • Final Coil of Bahamut armor (but not weapons)
Ifrit, Garuda, Titan, Moogle, Ramuh, and Bismark weapons have crafted versions available, though they're not technically replicas, as they have additional graphic effects.

Artifact armor (via alchemist-crafted items) have augmented versions (which are dyable), though they're also not technically replicas, and you need to turn in the original piece along with the alchemist-crafted items.