hmm for object that don't move like trees and houses i put the bottom part on the lower layer then the top on the layer above it. like so.

http://www.allegro.cc/depot/screenshots/3138_large.jpg layer 2

http://www.allegro.cc/depot/screenshots/3139_large.jpg layer 3

this way you can put you none passable zones and the base of the house or tree. when you do this it make the object appear 3D because the top part of the object will be draw after the player object so it will look like the player is be hide the tree.

thats not a problem ether. what you do is break your characters in to parts draw the parts on different layers. i am also working on a characters editor the works with characters parts. that is also for my MMrpg and is located in the depot.

I just sort my game objects by y coordinate and draw top down.

My big sticking point (and I have an idea for this that suits my engine, but it merits discussion here and I haven't seen it brought up) is brideges and things you can walk iver/under. Fenix Blade, as well as quite a few of the old SNES RPG's, can do this and it's very effective both in terms of looking cool and possibly making map layouts a bit more efficient.

Attached a quick montage for visual reference:

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Ideas on how to do that?

This is my thinking, yes.

I'm just going to babble here, but maybe it's some food for thought.

Why not have infinite layers? In fact, represent layers with Z (as in X,Y,Z). Each tile stores an X,Y and Z variable as well as b,t,l,r variable (bottom, top, left, right). Now, in your map editor, at any time you can pick which layer (Z) you are adding to. So you could have grass at Z=0 and Z=10 (where 0 would be lower depth-wise than grass at 10). Next, you set the b,t,l,r variables, which determine if you can pass the position of the tile. Alternatively, you could just use BB, but even with b,t,l,r I don't see why this would anger free movement (although it might get a little finicky at the edges).

Now here's the kicker: our player is at layer z. That's z, not Z. Meaning, the player is not on a static layer, but his layer actually changes. Say for example you go through a door, well the door has as underlying code that sets the player's z to its Z variable. Thus, in 23's picture (the far left one) above with the bridge and the door, say when you exit that door your now on Z=20 so z = 20. But, before z = 0, so you'd be below the bridge. There's still a bit of confusion in the collision, but maybe it's an idea.

[edit]
In the end, you'll have to sort your tiles from Z=0 to Z=highest in some kind of structure and then draw them going through your sorted list with the method above.

Final Fantasy IV.

And Onewing/Elverion pretty much suggested it the way I'd do it. Everything in my game is an object, sorted by z for layer and then y for objects on the same layer that overlap. Tiles would have triggers moving objects between layers as they pass over them. I don't know if that's how the old classics did it, but it's my way.

Now, how to draw transparent water over the player's lower legs when he's walking in liquid. Another trick some old classics (and Fenix Blade) did .... and one that still stumps me a bit.

I don't know, that sounds like over-complicating things. I've got two ideas:

1) The FFIV way (or some rpg game...). When over a forest tile, the lower half of the body turns translucent. This could just be code inside the player object, in which when the player is on certain tiles, the lower half is draw translucently (that shouldn't be too difficult to do) on top of the forest tile. Thus, when on a water tile, the player code knows to draw the bottom half translucently. Now, we still have the problem of the ripple effect. This is a special function in the tile object that basically is run when the player is moving on top of a water tile. This special function draws the ripple before the player is drawn, so the solid part of the player is drawn over the ripple, while the translucent part appears below the ripple, creating some sort of depth.

2) I scratched this idea as I was writing it.

Since I started this thread I'm using it for transfer of text. Feel free to ignore the following.

I'd just draw the normal water tile, then the player, then a translucent special water tile with ripples

I'd do it how Thomas suggested.

Oh by the way Rick: I thought that you're working on that isometric board game.

Hehe, me too, me too. That's why I abandoned the idea of isometric engine.

Yeah, I'm thinking that if I'm going to make RTS or RPG I'd go for normal tiles or switch to complete 3d.