Defeat Lavos at the end of Black Omen, and successfully complete the game to unlock New Game+ mode and the Dimensional Vortex dungeon.
Unlock the Black Omen in 12,000 B.C. The Lost Sanctum dungeon will now be accessible in 65 million B.C., and at certain locations in 600 A.D.
The second time you fight Magus, you are given the choice of "Yes, I want to fight you" and "No, I don't". If you choose "No", not only will you not have to fight Magus, but he will also join your party.
Successfully complete the indicated task to view the corresponding alternate ending:
Go to Guardia Forest in 600 AD. Once inside, take the first right, and go to the upper path. While in the small clearing, look for a bush in the upper left. Move next to the bush, and it will begin to shake. Press A, and a monster will pop out, leaving a Shelter as it runs away. Get the Shelter, then leave the forest, and reenter. Repeat this as many times as desired.
When on the Black Omen, you will encounter a Blubber Hulk (which at first looks like a tornado on the ground). Approach it, and have Ayla use Charm to get a Strength Capsule. Then, run away, and go back through the door you came through (with the two Nus), and repeat as many times as desired.
Money does not transfer into your next game in New Game+ mode. To keep your wealth, before facing Lavos at the end of Black Omen, buy everything possible from the merchants until your funds are exhausted. Visit the trader in the Prehistoric Era, and trade for as many of his items as possible. Then, defeat Lavos to successfully complete the game. In New Game + mode, your items will carry over. Sell all the unwanted items for money in New Game+ mode.