There are four notable side-quests. All of them contain secret combo summons guarded by powerful superbosses. The summons are all significantly more powerful than the other ones you find elsewhere, but also require more Djinn.
The side-quests are:
- Yampi Desert Cave, which, unsurprisingly, is in Yampi Desert. Accessing it requires Teleport and Sand, but by the time you have Teleport you will have every other Psynergy you will need inside.
- Sea of Time Islet Cave, which you will go to anyway if you follow the guide on the main page. You need Teleport to access it, as well as completing the trading game outlined in the guide.
- Treasure Isle, which is the island in the north part of the Eastern Sea, somewhere north of Izumo and east of Angara. It's surrounded by rocky spires which you can navigate around.
- Anemos Inner Sanctum, which is the seemingly inaccessible structure to the east of Contigo on Atteka. The teleport circle in the center of Contigo leads straight into the middle of the Anemos Inner Sanctum entry room, where all 72 Djinn from both GS games are required. You obviously need to complete the first Golden Sun and then transfer the data across, and you must also complete the other side-quests, because they all have Djinn in them that you need. You wouldn't think about facing the hardest boss in the game without every possible advantage either, would you?
All of these make the rest of the game significantly easier, although by this point the only remaining obstacle will be whatever you haven't done of Mars Lighthouse, which will probably only be Doom Dragon.