Below is a cset (color set) from a palette, I pointed this out because many people seem to confuse palettes and csets.
A palette contains several csets, where a colorset is just one line of 16 colors contained in a palette.
The cset below is cset 2 from the level palette above.

When You decide to section off your overworld into areas displaying different colors, like summer, or winter, what you are doing is choosing different level palettes to use in these areas.
Level palettes replace csets 2, 3, 4, and 9 in the main palette allowing you this deversity in color choices.

The Pure tileset Palettes seem to have a pretty good method to their madness.
By this I mean as you change from one level palette to the next the csets arranged as they are allow the tiles to be displayed in appropriate colors, which allows you to display one tile in several different colors, instead of having to duplicate that tile several times to display it in different colors.

Here's a look at how colors are aligned and used in the pure csets.

0, This first color is always tranparent.
1, This color is generally used to highlight colors 2 and 3
2, Used in the tree canopies, bushes, etc.
3, Used in the tree canopies, bushes, etc.
4, This color is generally used in shading colors 2 and 3
5, Light grass color
6, Dark grass color
7, Light flower colors (pedals)
8, Dark flower colors (bud)
9, Mountains, tree trunks (light color)
A, Mountains, tree trunks (darker color)
B, Mountains, tree trunks (darkest color)
C, Lighter shade of D and E for highlighting.
D, Bushes, Tree canopies
E, Bushes, Tree canopies
F, Always Black

Of course I didn't show how all tiles are used, but just gave a general idea how grass, bushes, trees, and mountains are used, so as you change from one level palette or even a cset in the same palette, then those tiles draw on the same cset position to get their new color. Heres another example, these flowers below are all the same tile, just displayed in csets 2, 3, and 4 from the "ow regular" palette above, they draw from color numbers 7 and 8 in the palette for the bud and pedals, and colors 5 and 6 for the grass.

Dungeon Palettes are set up a little differently than the overworld level palettes.
Instead of the last color in a cset (F) being black another color has been added.
The black can often be found in the second slot (1) but not always.

(colorset 2)
0, This first color is always tranparent.
1, Normally but not always black
2, walls, doors, ceilings, floors
3, walls, doors, ceilings, floors
4, walls, doors, ceilings, floors
5, walls, doors, ceilings, floors
6, walls, doors, ceilings, floors
7, Torches, statues, floor triforce, fire, door trim (Light color)
8, Torches, statues, floor triforce, fire, door trim (Dark color)
9, Floor boarder (darker color)
A, Floor boarder (lighter color)
B, Statues, Torches, Spikes, (light color)
C, Statues, Torches, Spikes, (darker color)
D, Statues, Torches, Spikes, (darkest color)
E, Boiling pots, books, bottles
F, Ice

(Colorsets 3 and 4 you can see the dark and light water and lava and their placement)

In addition cset 3 and 4 are most often used for light water/lava, and dark water/lava.
This results in one problem for me, I like different floor colors, and using just cset 2 for both floor and wall pretty much forces you to use the same colors on wall and floor.
What I do then is choose which water colors if any I'm to use in the dungeon and then I replace the other with a cset that I want for my floors.