Dream Gem

Like the Dream Gem in Muse's Dream?  I do too considering it gives 18 Magic Defense and protects against sleep.  To keep the Gem, equip Sharl with it and have him killed (0 LP).  He will disappear from your party.  After exiting the dream, talk to him again, and he'll join you.  Now you can unequip the Dream Gem from him.

LP in the Final Dungeon

I don't know if this can be considered a secret or not but, in the Final Dungeon, if a character's LP reaches 0, they will not die and be removed from the party.  Instead, they will be completely healed.

Harid and the Seven Star Sword Trick

This trick is very well known by now.  If Harid isn't your main character, the best sword that you may have in his 1st slot is the Falchion.  This can be changed- after you get the Seven Star Sword from the Divine Church by killing Maximus, place Harid in the Tiger Cave formation in the same position as in the screen below:

Equip the Seven Star Sword on him in his second slot and enter Commander Mode.  Fight in Commander Mode having your characters use Focus.  Harid will eventually learn Starburst and another Seven Star Sword with an Attack Power of 60 will appear in his Scimitar slot.  Don't remove it, or its attack power will revert to 35.  Also, don't use Starstream or the same thing will happen.

Inner Eye

This one is just weird.  If your character is blind and tries to use Random Arrow, they will use the secret bow waza, Inner-Eye Random Arrow.  This waza has 100% accuracy but costs 18 WP.

Stealing Hands

Alright, this isn't exactly a secret, but it's still nice.  If your Big Sword user learns Stealing Hands, they can steal the weapon of an enemy that attacks.  Of course, long range weapons and the Dragon Spear can't be stolen in this way.  (You thought it would be that easy to get the Dragon Spear?)

The Silver Hand

The Silver Hand can be found in Muse's Dream.  It's primary function seems to be giving Sharl his paralyzed hand back, but it has another purpose.  If given to a character without a Shield, the Silver Hand can cause the user to attack with 2 equipped weapons (the weapon chosen and the next weapon) with the following requirements: 1)The user does not have a shield equipped. 2)The user is not using a 2-handed weapon to attack. 3)The user is not using a hit-all waza. 4)The next weapon inline is not a 2-handed weapon. 5)-Harid only- The first weapon will always be the 1st slot. Using this trick, you can make a devestating attacker (such as Harid with the Seven Star trick.)