After you've resurrected the five towers in the underworld, you can go to a small cave located west of Tower 5. Kill the guards inside, then either use an ice ring or throw pots at the fire-swirling monsters that you can't reach. This means you can visit Polynesia, one of the islands near Yunkou. You can sleep there and where you can take a nap for free. You'll be burnt in the morning, and your 'Macho Appeal' raises by 10. This has no relevance to the game.
Not as well known as the one above, the cave is located north of Tower 3 and looks like a small cluster of snow. Simply throw the rocks blocking your path out of the way to get to the control room. Mu features in Terranigma's predecessor, Illusion of Gaia/Time. It was one hard level. The importance of resurrecting Mu is that as the surface world and the underworld are linked, Mu will be resurrected in the other world as well. This means you can visit Mu in the surface world where you can obtain one of the four special weapons - the EnbuPike.
Not an important secret, but some don't know of it. Did you know that you can throw pots/pumpkins at certain people in Crysta, and hit them? Like go into the house to the left of the weavers and into the room on the right. Pick up the pot in there and chuck it at the boy. He'll be well annoyed at you and tell you so. This also works for the boy outside the house mentioned above, chuck a pumpkin at him. Most people in the elder's house can be hit as well. You can even get a three-in-a-row by power-throwing a pot at the people sitting at the table! They'll spin round, then complain. The only other time this seems to work is in Liotto. One of the houses has a monkey that does the Samba. Throw a pot at him, then talk to the woman sitting opposite him.
When fighting the Parasite in the Ra Tree, it'll eventually shoot some orange claws at you during its second attack. These are worth about 55 Experience points! Simply kill them all, then wait until they're spit out at you again and repeat. Thanks to Dais for this information.
When you first enter Louran, you'll undoubtedly meet a man who doesn't know what to do with his money when he dies. Tell him to take it with him to his grave. When the town turns into a zombie-infested ruin, go to the cemetery. One of the graves has 500 Gems with your name written all over it.
When you first enter Castle Sylvain, pick a fight with a Cursed Armor in the second room and then have it follow you up the stairs towards the painting when you are almost dead. If you timed it right, you can still walk around after death! The effect will wear off after leaving the room, however, and you can’t do touch or attack anything. Click the link above to see a video of this glitch in action.
Pretty well known this one. Visit the Quatto's, originally south of Litz but they move later on to the north of Liotto, and go into the northwest tent. Talk to the woman inside and she'll ask you for a massage. Agree, then push into her back. She'll say something like, "ooh that's good!". Keep pushing and eventually, she'll tip you 1 measly Gem. But every time you do it after that, she'll tell you that you've improved and give you 5 Gems. Try pushing her front, she'll have a go at you, telling you not to get fresh!
Some people are unsure what to do with the Fever medicine given to them by the Litz doctor. Well, once you've economically progressed Suncoast far enough, you'll find a Japanese couple upstairs in the inn. The bloke is in bed sick with a... guess what... fever, so equip the medicine and talk to his wife. You'll get a MagiRock for your troubles.
You'll find a couple in Yunkou who abandoned their daughter Chija at birth. Tut tut. But they want to know how she is, and it just so happens you can help. Make sure you have a Pretty Flower from the woman in Loire, then go to the Nomads near Louran. In one of the tents (I think it's the upper-right one), you'll find a small girl. Equip the Pretty Flower and talk to her. Hmm... seems a bit thick really. Oh well. Go back to Yonkou and tell her parents. Then go back to see her at the Nomads again, then all the way back to Yunkou and talk to her parents again. And what do you get? A MagiRock. Yippee.
There's an empty lot with a trash can next to it in NeoTokio. Go inside the trash can and you'll appear in a messy room. A ghost appears, which you must beat, the best way to beat it is to use Pyro Rings. When you beat it, a chicken will appear and thank you. You'll then be transported back outside the can, the empty lot has now been replaced with a building where you'll be able to meet and talk to Quintet, the Terranigma team who are the dudes who made, designed, etc. the game you're playing!
Expand Freedom a bit, and go to the shop. Go down the flights of stairs to get to the basement. Oh my, it's a black market! And they've got the KingBird as a prisoner! Once again, it's up to you to sort things out. Talk to the guard a couple of times and then pay him 5000 Gems to release him. Then, go to the KingBird's nest at Sanctuar and he'll have a MagiRock for you. Bless him. The best way to get money is to head for NeoTokyo sewers and go left, then fight the dog-like creatures to get between 300-350 Gems. Thanks to Ferme for the information on the Kingbird's release cost and money-making methods.
Some people don't know about this either. You need to expand Loire to the max. Go to the second avenue, then east to Loire Realty. Buy an apartment at the Rococo building for 800 Gems, then go next door to the furniture shop attached to Loire Realty, called Michelle Furniture. You can buy the following furniture for your house: rug, bookshelf, desk, shelf, and dresser. Each for 100 Gems. Then go west to get to the Rococo apartment and use the Apartment Key on the first door on the right. Your new home, furnished and all! You can save and sleep to regain energy here.
Enter the circled area just north of Loire next to the bridge and you'll come across a shack. The old guy inside explains that he races chickens. Leave his house and go off the screen to the north to get to the chicken races. Give 10 Gems to the woman next to the counter to get a tip for the winning chicken, then talk to the bloke at the counter to make your bet. Depending on the odds and of course, picking the winning chicken, you can make off with a load of cash, up to 800 Gems if the odds are 16 to 1. Much easier than killing monsters for money!
Speak to a bloke north of Alaska and he'll talk about different migratory paths of gulls. You can travel using these gulls if you find certain places called Stopovers. The migratory paths are: Alaska to Australia, N America to Kamiyo, N America to Savannah, and S America to Greenland. The one in Alaska is to the northwest corner and takes you to just north of Suncoast. The S America one is Southwest of Liotto, and takes you to Greenland just north of Penguina. There are also three in the Kingbirds nest in Sanctuar. The left one takes you to the Savannah, the animal paradise. The middle one takes you to Kamiyo, on the island of NeoTokyo. The right one takes you to the Windvale cave.