All three items can be acquired a number of ways. You will automatically receive 99 Dark Matters at the Monster Arena after capturing five of every Fiend, although you can also obtain the item as a rare drop from pretty much every Area Conquest, Species Conquest, and Original Creation at the Arena as well. You can also Bribe them from Land Worms inside Sin. As far as Supreme Gems go, they are rare steals from Sin's Left Fin, Sin, and Seymour Omnis. They are commonly dropped by Jormungand at the Arena, and can be Bribed from Halmas in the Omega Ruins. Finally, you will automatically receive 60 Supreme Gems at the Arena after capturing two full species. Stamina Tonics can also be acquired easily at the Arena; they are commonly dropped by the Abyss Worm. Stamina Tonics are also sometimes stolen from Macheas (Omega Ruins) and Catoblepas (Arena). They can also be Bribed from Iron Giants (Thunder Plains) and Gemini (Omega Ruins/Inside Sin). Lastly, you will automatically receive 99 Stamina Tonics after capturing at least one of every Fiend on Besaid Island.

Quote Originally Posted by icysummoner
But about Omega - I can't remember if I actually defeated him before or not, but if I did not defeat him, will he still be there in the Omega ruins?
Omega Weapon will not disappear from the Ruins until it is defeated.