Overworld-
1. Make a dungeon entrance where once you get some sort of magical powder, you sprinkle it on a strange plot of land (led there by the story obviously) and the dungeon appears out of the ground
2. (This applies to overworld because after reaching this new area, you could activate a switch there that allows you to get back to the normal overworld) After beating a certain dungeon, your told to go back to a previous one. When you enter, there is a new path to take and doing so takes you to a new area out of the dungeon. Lets say this all takes place in a forest, then it would take you to a deeper part of the woods. here you see 3 unlit torches, and one screen up lies a bunch of rubble from an old temple. You have to go to a few screens, awaken old statues so that the torches light up once more. then once they are all lit, play a song to make the fires truly awaken. (EX: Song of Awakening) After this, the fire from the torches make the ground rumble because it lifted an old tower for the goddesses were the temple rubble was
Dungeon-
1. you find an old shipwreck that lies beneath the beach. Upon entering, you are greeted by a few of the ships dead crew members who are surprised to see you, but still tell you to turn back. you dont, and continue. After reaching the mini boss, you find out that its actually all the old crew members who came together to form a giant monster. after defeating them you get the dungeon item.... a gust jar. This will let you suck up sand that still lies around the wreckage. this allows you to reach the boss.when you enter the captains chamber which is the boss room, a guy who you talked to before entering the dungeon runs in and says that he is the captain and was the only one to escape. he knows what your looking for so he challenges you to a fight. I dont know how the fight would work, but it was just an idea i had)
2. After an encounter with the main enemy of the game, you awake in the past where an old temple lies nearby.When you enter, the place which is actually a knights training ground and it looks well taken care of, and so you fight the mini boss which is a knight who stops you for trespassing. After this, you get the magical harp from OoA. your then sent to the beginning. In the present, the your guider of this game tries to talk to you, and says that the harp lets you go through time. you use it to go to the future where the door to a now old knights training ground is open for you to enter. After reaching the halfway point, you will reach a now accessible outside area where you can use the harp. this last half of the dungeon requires you to keep switching through time until you finally reach the boss. The boss is in the present this time and after killing it, you get the next thing that you need
3. In the Royal graveyard, you reach the Kings grave. (this dungeon takes place in the past since its after the knights training ground) The kings grave is full of statues of the king. after reaching the mini boss which is an old Deathnut, you get the hookshot. The final boss is the Kings ghost who has a shield where when ever he has it out, you use your hookshot on it to lower his defense.
4. The last dungeon which is Hyrule castle, and it has the torch mechanic again, but this time there are 8 torches representing the 8 previous dungeons. Each part of the castle represents a different one. after lighting the 8 torches, the mini boss appears and then you can proceed after beating him. This gives you access to the kings chamber which is the entrance to the 2nd part of the final dungeon. The second part is.....
5. Below Hyrule. This dungeon is the largest one in the entire game, and is meant to occupy the entire space below Hyrule and all its other dungeons. its an elaborate cave system that test your skills that you have learned and making you apply them. At the end, you reach another boss which is actually a mini boss. After beating him, you reach the 3rd and finnal part which is.....
6. Hyrules Tower. This is an ancient tower that can only be accessed in the past. Once making it out of below Hyrule, you play the harp to enter the tower when its not blocked off. halfway through you are able to change to the future where you finish the climb and fight the true final boss
Sidequest-
As a side quest, you are sent to the normal graveyard. (yes there are 2) When you come here after reaching an old text under the village elders house, two Ghinis will be seen talking to each other. They are talking about you and how your trying to stop the main bad guy. They then see you and start attacking. After killing them you receive the Hero's key which is used on the Hero's Gate here in the same graveyard. beyond the gate lies the old Hero's of Hyrule. reaching the biggest grave causes one of the hero's to wake up. he is surprised to see you and tells you that to access the hero's secret, you must prove yourself worthy. He send you on a quest that last up till the end of the 5 dungeon. He tells you to find the 8 Hero Gems of Hyrule and bring them to him. doing this rewards you with the entrance to his grave which not only holds one mini boss, but 2. Traveling though the first part, you come across the latest hero before you. He challenges you to a duel. doing so allows you to progress to the next part. halfway through you find another mini boss which is the 2nd latest hero before you. hes tougher, but after beating him you can finally move on. The final boss is the oldest and greatest hero, and after beating him he rewards you with his Sword and old tunic to prove that you are the true new hero.
*I know its a lot, but I have to say it somewhere because I suck at using Zelda Classic, or at least actually applying these ideas to dungeons