Welcome to this guide in progress :) Feel free to contribute your own findings or point out criticisms of what's already here. Secret/Hidden quests are defined as NPCs or items giving quests that have no yellow symbol above them or on the map or the glowy stuff like blue etc. Hope you find something fun here and have a good day <3

This guide is in chronological order of leveling process from lowest area to highest area fyi.

Go around the left side of the house where my cursor is:
follow the deck:
jump in the window:
clicky clicky:
pick it up and activate it from your inventory:
Get supplies: rope & wood:
Fix up the bridge:
Kill the zombies & Fat Man:
Now die to get to the next secret.
(after checking out this sweet box ReeVize noticed :)

the portal with the archway is the portal to the dungeon, the other one takes you to Lambda Abyss
to get past bridges, must kill minions, this will be the first area
The first boss : Soma Giant (no loot at this time)
The second boss: The Red General (lootable eDna)

Treasure chest in Fire City near the skill spiral gives a few "contract" quests
Have fun taking orders from a box ;)
1st contract:
2nd
3rd
4th
5th
6th
7th
8th
You will also find a quest chain that has the yellow marker but is kind of hidden, it's a side quest I suppose but adding here via Thargor's mention.
It is found here:
Here's the boy:
Here's an image of the cutscene:
Once you make it to 14 that questchain breaks.
Here's some of the quest text from it to give you a preview, there has been expressed concerns that this may possibly be the to be released quests for later, one day we will find out.

Thanks to Janinne/Carpe.noctem for these screenies: (click on wine glass)
(which can be found here on the map)
This is what this quest is:
Step 1 of quest:
Step 2 of quest:
Then there's this book too
That gives you this quest:
Then this quest:
Then this 3rd quest:
The knight starts with obvious quests & yellow marker, but then after thats done he actually has some more for you:

Know anything in addition? Please link some screenies and let me know :) And keep an eye out as you never know what you may find!

Thanks for reading, please rate kindly :)