Dungeons:

There are six main dungeons ("triforce" dungeons), twelve secondary dungeons (the main dungeons in the wrong time periods), four optional dungeons (the item inside each is still highly recommended), twelve class dungeons (each class only can access six of them), and level 7 that ends with fighting Ganon. If you beat the game but need to know more, read the end level 7 walkthrough or go to the end of game section, but only after you've beaten the game.

Level 1: Forest Hideout.
Not really in a forest, but I didn't na- uhhh, never mind. Easy set of dungeons to start out with.
1-1 Present
1-2 Past
1-3 Future

Level 2: Desert Fortress.
Just imagine what it was like before the sand covered it up. Please? I'm not going to draw it for you. Almost straightforward. There's a switch that you can't get to you when you need to.
2-1 Past
2-2 Future
2-3 Present

Level 3: Flatlands Cavern.
More boring than the last place. Slightly less dry. To get through 3-3 future, you need the bow from a shop and the wood arrows from 3-2 past.
3-1 Present
3-2 Past
3-3 Future

Level 4: Jungle Labyrinth.
Is it a real labyrinth? It will get confusing, so maybe. Each of the three dungeons moves back and forth between time periods.
4-1 Past
4-2 Future
4-3 Present

Level 5: Calatian Monastery.
Did anybody know how to spell monastery? I'll admit my first guess was wrong. There's a switch in 5-1 Past that lowers the statues in the overworld, unlocking the entrance to 5-2 and 5-3. The main dungeon might be the one that takes the most time to beat.
5-1 Past
5-2 Present
5-3 Future

Level 6: Flooded Temple.
Icy, swampy, wet. The first two are pretty normal. The main dungeon is split into two pieces, and you have to raise the water level in each to get to the end.
6-1 Past
6-2 Future
6-3 Present

Level 7: King's Bunker.
I'm just treating this as a mashup into a single dungeon. You'll see why. Start out by going there in the past.
7-1 & 7-2 & 7-3

Optional Dungeons:
Optional Level O1: The Screaming Skull
Optional Level O2: Jack the Giant Killer
Optional Level O3: Devil Fish
Optional Level O4: The Day the Earth Froze

Class Dungeons (optional):

1st Future (requires Magic Boomerang)
1-1: Monk & Knight
1-2: Thief & Wizard
1-3: Thief & Knight
1-4: Monk & Wizard
2nd Present (requires Ladder)
2-1: Monk & Knight
2-2: Thief & Wizard
2-3: Thief & Knight
2-4: Monk & Wizard
3rd Past (requires Silver Arrows)
3-1: Monk & Knight
3-2: Thief & Wizard
3-3: Thief & Knight
3-4: Monk & Wizard