Part 1: Millennial Fair and Guardia Castle
We can find something hidden almost right away. In Lucca's bedroom there is a strange, blocky, circular pattern hidden under the floor. This pattern scrolls quite quickly, moving up and to the left. Interestingly, this pattern only appears in Lucca's bedroom and in no other room in her house. This is not the last we'll be seeing of this pattern, though, and when we see it again we'll understand what it is and why it's here.
This one's a little strange. If we go into the ticket office in Truce we can see there's a cat sat underneath the desk (up and to the left of Crono's head). It doesn't appear to be used in any cut-scenes or events, so why put it there?
Some of the houses in Porre have small bits of misplaced floor. The mayors bedroom (left) has a piece of carpet in the wall, and the Snail Stop has a small portion of floor which is usually hidden underneath the black. In the picture it starts to the right of Crono and stops to the right of the pianist. These are not the most interesting points in the world, but are worth noting anyway.
As an aside, this is the only time I will demonstrate this particular scenario. There are many buildings in the game that have one or two tiles of misplaced floor, but unless it's particularly interesting I won't comment.
Here's that strange background again. It only appears in this screen of the fair and no other, very similar to Lucca's house. Unlike Lucca's house, this time the background scrolls at various speeds and various directions, apparently changing at random.
You can also see the warp point hidden beneath the scenery, waiting until it's supposed to be used.
When we first drop into Truce Canyon we see the background again. This time it keeps scrolling up and to the left at a slow, steady pace.
Another sprite hidden under a counter. This time a little Spekkio is hidden in the shop in Truce circa 600AD.
In the western tower of Guardia Castle there are two treasure chests hidden in the top left corner. Quite what they signify I don't know. I did think they might be a way of checking which chests you have/haven't opened inside the castle, but as far as I can tell the chests always look like this.
In the cathedral we can see four blue fireballs hidden under the floor. These fireballs are the places where the nuns stand when they change into Nagaettes. Once they have changed, however, the fire goes away. This effect is also used at other points in the game, such as the room beneath the cathedral where three Gnashers disguise themselves as humans.
People familiar with the game may recognise this room. If you attempt to grab the bromide (signified by the white circle on the desk) you will be interrupted by three Hench's. In the image on the right we can see that the Hench's are always outside the door in their "moving" animation, only showing themselves if you grab the item.
Another interesting thing about this room: If we peel away even more sprites we can see a little Spekkio sprite! Comparing the pictures, we can see he's hidden under the dresser where the bromide is. If you grab the bromide, Spekkio vanishes. This shows that he's being used as an indicator of an event handler of some kind. This is not the only time he is used like this. In fact, he's also hidden underneath several doors in the game, used as a means of deciding whether to display the "open" or "closed" door sprite.
Meanwhile, on the eastern side of the dungeon, we can find something hidden in the room with the partying monsters. If we peel away the wall we can see some pillars, a window and a spare bit of tile floating there. It's not possible to interact with any of this stuff, however.
The only other interesting hidden items in this part of the game are ones I've already illustrated. There are several hidden Spekkio sprites, a few hidden fireballs and that strange background appearing in the easternmost part of Guardia Forest. Since I've already shown what they look like I won't do so again.