There are a several sort of "secrets" in Harvest Moon: Back to Nature. These are things that aren't well known and that you might not figure out on your own just by playing the game.

The Harvest Goddess

The Harvest Goddess

If you throw a crop you grow or some kind of animal product into the pond by the waterfall the Harvest Goddess will appear and thank you for your gift.
If you throw 5 items in she will give you a Power Berry. If you throw in 10 items you'll get an affection bonus with the girl who likes you the most. And if you throw in 20 items she'll give you a special kind of lumber that you automatically sell to Gotz for 1,000g.
If you continue to give her gifts in this videogame she'll give you days with good weather.
The Kappa

The Kappa

If you throw cucumbers into the lake on the mountain where the Winter Mine is a Kappa will appear.
It will only appear after 11:00 am during the spring.
Kappas are creatures from Japanese mythology and they love Cucumbers. If you throw 3 cucumbers into the lake the Kappa will give you a Mystic Berry.
The Hot Springs

The Hot Springs

The Hot Springs in this videogame are by far the best way to recover stamina and to restore fatigue. For every in game minute that you're inside the Hot Springs you'll recover 2 stamina and have 1 fatigue removed.
You can stay up super late, jump in the Hot Springs for about an hour at around 4:00 am, run back to your farm and be in bed before 6:00 am. This will have a better effect on your stamina and fatigue than going to sleep at 6:00 pm and you'll be able to get a ton more work done each day.




Inside the Harvest Sprites' home  

Relaxation Tea Leaves

On any sunny, non-festival day during the spring visit the Harvest Sprites between 3:00 pm and 4:00 pm. Give them each a gift they love, Flour is probably the easiest. You have to give them each an item without leaving their house.
After you give them the gifts they'll invite you to their tea party. At the end of the tea party they'll give you Relaxation Tea Leaves which you can use to make Relaxation Tea.
If you submit Relaxation Tea for the Cooking Festival in this game you're pretty much guaranteed to win.
     
Where to stand to get Spa-Boiled Eggs  

Spa-Boiled Eggs

A lot of the characters in this videogame really love Spa-Boiled Eggs. To get Spa-Boiled Eggs take regular or Gold Eggs to the back of the Hot Springs and throw them in. You'll immediately receive a Spa-Boiled Egg.
The screenshot shows exactly where to stand to throw the eggs into the Hot Springs.
     
Meeting Kai on the beach  

Perfume

After a hurricane happens in the game you can visit the beach where you'll find Kai. There will be an event where you get an affection bonus with Kai and you'll get a choice between receiving a bottle or Perfume.
To trigger the event you need to have at least 120 affection with Kai.
The bottle is useless but the Perfume makes a fantastic gift for the girls.

Item Shipping Prices

This is a list of all the items in the videogame Harvest Moon: Back to Nature that you can ship and the prices that they sell for that you can use as a quick reference if you want to quickly look up a specific item or something.
 
Crop Selling Price
Cabbage 250g
Carrot 120g
Corn 100g
Cucumber 60g
Eggplant 80g
Green Pepper 40g
Magic Red Flower (red) 200g
Onion 80g
Orangecup Fruit 60g
Pineapple 500g
Potato 80g
Pumpkin 250g
Spinach 80g
Strawberry 30g
Sweet Potato 120g
Tomato 60g
Turnip 60g

Fish Selling Price
Large Fish 200g
Medium Fish 120g
Small Fish 50g

Animal Products Selling Price
Cheese Small 300g
Cheese Medium 400g
Cheese Large 500g
Cheese Gold 600g
Egg 50g
Golden Egg 150g
Mayonnaise Small 100g
Mayonnaise Medium 150g
Mayonnaise Large 200g
Mayonnaise Gold 300g
Milk Small 100g
Milk Medium 150g
Milk Large 200g
Milk Gold 300g
Spa-Boiled Egg 80g
Wool Small 100g
Wool Medium 400g
Wool Large 500g
Wool Gold 600g
Yarn Small 300g
Yarm Medium 700g
Yarn Large 800g
Yarn Gold 1,000g

Wild Plants Selling Price
Apple 50g
Bamboo Shoot 50g
Blue Grass 100g
Green Grass 100g
Honey 50g or 60g*
Mushroom 70g
Poisonous Mushroom 100g
Red Grass 100g
Truffle 500g
Wild Grape 50gs

Ore/Jewelry Selling Price
Adamantite 50g
Bracelet 2,000g
Copper Ore 15g
Earrings 2,000g
Gold Ore 25g
Junk Ore 1g
Mystrile Ore 40g
Necklace 2,000g
Orichalc 50g
Silver Ore 20g

*If you give a jar of honey to Louis in this game he'll tell you the bees are of a rare species and the honey you collect will then sell for 60g instead of 50g.
I realize the SUGDW Apple isn't in there because I wanted to keep my tables symmetrical. It sells for 50g like a regular Apple.
 Mirai Nikki

The girl with the sharp thorn in her flesh
I meet you at your story
Behind the hatred there lies a murderous love

Do you kill your friends, if you can fulfill your wish?
Can you die for someone?
They are synonymous words

Life is a game. It's a survival. That's right! How do you start?
Time and Space, It's a crossroad through a gate! Where do you go?

You seek eternal breath
Why do you need to live?
We don't know when this world came into being

Mirai Nikki
Consentes Dei Juno Jupiter Minerva Apollo Mars Ceres
Mercurius Diana Baccus Vulcanus Pluto Vesta Venus

微睡の淵で目蓋に揺蕩う

夢想の神は優雅に微笑み死を降し
時空を総べる因果の鎖は絡み出す

神の与えし空想 Program

さぁ eins zwei drei! 重なり合う
さぁ eins zwei drei! 死を躱して

消滅の遊戯に焦がれる奇跡を奪う Survival Game
螺旋のように

Consentes Dei Juno Jupiter Minerva Apollo Mars Ceres
Mercurius Diana Baccus Vulcanus Pluto Vesta Venus

泡沫の未来書き換えるように

空想繋ぐ論廻のノイズが鳴り渡る
時間は歪み因果の旋律は崩れ去る

神の与えし継承 Program

さぁ eins zwei drei! 連なり合う
さぁ eins zwei drei! 死を振り切って

消滅の遊戯に抗う奇跡に挑む Eraser Game
夢幻のように

神の与えし機械(からくり) Program

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