Items Sold - Iron Blade, Steel Blade, Silver Blade, Physic, and Unlock.
The second Secret Shop is at the bottom right hand corner of the map, and is far better in my opinion. Of course, you need the Physic's for later, but the bottom sells quite a few good items as well. You should buy 1-4 Physics, as many "Killer" weapons as characters that you use. Buy 1-3 Elixers and 2 Lockpicks.
Items Sold - Killing Edge, Killer ?Lance, Killer Axe, Killer Bow, Elixer, Chest Key, and Lockpick.
The next Secret Shop is on Chapter: Kinship Bond. In case you didn't have enough money earlier or if you forgot, this Secret Shop contains quite a few items of the last two Secret Shops. If you like a lot of the characters who have low resistence, or you just want to make sure you beat Cog of Destiny, buy 2-3 Barriers.
Items Sold - Elixer, Chest Key, Lockpick, Physic, Torch, Unlock, and Barrier.
The next Secret Shop is worthless in my opinion. It appears on Chapter: Four-Fanged Assault. It's either on the Forest on the island on the right of the map OR on the Forest that appears near the middle of the map. The only thing useful there is the Ocean Seal and only if you forgot to find it in Nabata Desert.
Items Sold - Armorslayer, Longsword, Heavy Spear, Horseslayer, Hammer, Halberd, and Ocean Seal.
The next Secret Shop is the on the bottom of the screen where there are four squares on Chapter: Sands of Time. You need a Warp staff to reach it AND it only sells promotional items near the end of the game.
Items Sold - Elysian Whip, Guiding Ring, Knight's Crest, Hero's Crest, and Orion's Bolt.