When mapping wilderness, the first step is always to put down a layer of *something*. Grass, water, marsh, whatever. And it always goes on the first layer, no exceptions. Basically, anything that fills up an entire square can and should be put on the first layer - it allows for much greater detail later. Next, figure out what, if any, landmarks you want. I generally like to include a river or creek in at least one of my maps. If you decide to put a creek in, make sure that either the player can get across to the other side, or that you have a good reason for not letting them (i.e., that shiny chest over yonder that they're not allowed to get 'til later.).
Please remember to keep a good reason in mind for most things you place on your map. Why did you put a million tiny puddles/ponds in your forest? "Just because" really isn't a good answer, and it tends to make the map look worse for it. "Because the forest is filled with depressions left from giant creatures and they collect rainwater for the locals" is a much much better reason and makes the map make sense (just make sure the player knows why, too.)
Having a lot of rivers makes a map more fun and interesting, but remember that they have to start from somewhere. At some point, if you do each map as a piece of a whole, there ought to be a mouth of a river somewhere. Rivers are fed indirectly by the ocean - tiny fingers lead from the ocean to a big lake, which then feeds the appointed river.
More often than not seeing two rivers near each other is because one is a branch of the other.
But, keep in mind that your game (statistically speaking) will probably be based in fantasy. If continents can fly in the air, then by golly rivers can start on top of mountains. I'm just saying you should be
aware that stuff like that doesn't happen in real life. Explaining how or why something is the way it appears in your game can add a lot more depth.
But with that said,
Waterfalls must gravity. Don't try to put a waterfall in the middle of a map without a cliff behind it! It's more understandable to not have a cliff if you just use teensy ones in a creek - those are extremely common and arise from small changes in the riverbed. But anything bigger than one tile and you need a cliff! The autotile itself proves this - the sides of it correspond to cliff edges.
Likewise, however, make sure the waterfall is actually FED by something. Waterfalls don't just sprout from nothing! If it's coming off a big tall mountain, it's probably fed by melting snow. If it's going into a valley, it's probably fed by a river or lake.
Mountains, cliffs and other riffraff ought to be *mostly* asymmetrical. Why? Because symmetry is a man-made invention to make things stand out. (Yes, I realize that nature does have *some* symmetry. But it's not very much.)
The symmetry that I'm talking about refers more to
excess symmetry moreso than
general symmetry, and most especially
vertical/horizontal moreso than
diagonal. In a medium such as this where there's only so many ways you can do something (due to the 32x32 grid) it's nearly impossible to completely avoid some amount of symmetry. (OMG there's a plant on the same row 234 blocks across!

)
On that note, do things in 3's. Why? Because even though symmetry should be avoided, the eye tends to ignore triangular patterns unless it's specifically looking for one. Lines will always stand out more. And also, it's just simply more aesthetically pleasing.

<-Decent example.

<- Not so great example. WHY IS EVERYTHING IN LINES!? Is it a mountain/weed army?!
DetailsAlways try to make a map visually interesting, and if not interesting, at least make it noteworthy. Have something interesting happen there (Remember
Toma's gravefrom Chrono Trigger? Do you remember that map? Literally all it was was a panorama, a teensy bit of cliff, one tiny rock and the grave. But the act of pouring soda on the grave was what made it noteworthy.)
If you're going to be asking for critique on the map, though, let us know what's going on! Don't assume that anyone knows that your ultra-awesome mega death scene takes place there. If it's boring, we're going to call it like we see it.
There is, however, such a thing as adding too much. Too many piles of grass, too many flowers, too many trees. Trees need space to grow - though some do grow close, if you've ever been in a forest you'll know that not only can you just about always fit between trees (even if you're on a bike or obese), but that double trees tend to be just that - trees that were so close that they grew together (or one tree that split). Most flowers can only grow where there's a decent amount of sunlight - that's the reason snapdragons tend to line paths instead of being everywhere in the woods - so don't go putting in bunches of flowers underneath a heavy patch of trees.
HOWEVER. Trees tend to look better, at least in RMXP, when they're placed fairly close together. Not *on top* of one another, but fairly close. Enough to make a barren field look like a dense forest or a lush jungle. Use layers to your advantage.
The "shadow grass" autotile is a godsend. While it is, technically, a "shadow," it can be used most anywhere just to add a tiny bit of detail to your map. I do, however, suggest that you don't use it too much in w~i~de open spaces.
Don't feel the need to be constrained by autotile usage just because of its name - for instance, I humbly believe that 030sn_ground01 (the snowy "ground" autotile) works marvelously as a frozen over creek - much better than the ice autotile the game gives you. However, whatever you decide to use an autotile as, don't use it as anything else -it'll just confuse players. The dirt autotile, however, is perfect for both beaten path and....well, beaten anything. Town square? Use it. Pig sty? Use it. Dry farm town? Use it. What exactly is the grass hanging onto in the middle of a serious drought? Answer: Not much, and by the time the cows have eaten most of it it's buh-bye grass and hello dustbowl.
I'll tell you a secret: This is the first time I've ever mapped a swamp that I didn't think was terrible to the nth degree. So, take a look at it: I've noticed that in gross, swampy water, there's always stuff in/on it - leaves, bugs, lily pads, algae, etc. Notice also that I've used the fallen leaves autotile: It seems counterintuitive, since the trees have no leaves that could fall (and look quite, quite dead), but I figured that that was probably the leaves of yore as well as the other plant life, fungi, mildew, other gross stuff..... But note that it's mostly centered around the trees themselves, mostly because the mapping doesn't allow for it to go right next to the water but also because in the event of a heavy rain, the water would just wash it away anyway.
PanoramasBasically, if you can see it on a flat grass map, you're doing it wrong. Remember that you're looking at the earth from a...eh, 45 degree angle or so. I'm ever so slightly against using it on an ocean map, but perhaps on a beach where you can't go anywhere else it would be ok. The only reason for seeing it is because...well, you can't go any farther. There's a drop. You're on a bridge. You're in the air. If it's flat, you can't see it, and thusly your chosen ground should cover the entire map.
HousesRemember these two factoids: On farms, houses are built almost wherever you please, because they're on a farm and generally set away from the main road. In a town or city, houses are generally set right near the road, and tend to be in a row. Cities are made to cram as many people in as they can, because that's where jobs are (post industrial revolution). So to deal with housing, houses are built cheaply (except for the owners of the factories, but I'll get to that in a second) and are packed together. This is what makes a city stop being a tiny nothing and become a city. Businesses and people. Towns are the same but on a smaller scale. Fewer businesses, more spaced out houses. And if you go to some booming international cities, you'll see even *more* people crammed into tiny spaces. So, if you're following this logic, houses out in the middle of nowhere can be HUGE, while houses in the city can be no bigger than a single sad room.
By Final Fantasy (and most other RPG's) logic, a good town is 2-3 houses, a shop, an inn, and one or two other specialty buildings. Keep this in mind - while it may not be everyone's cup of tea, it cuts down on clutter and the amount of maps (and time!) you need to spend on each town.
As for rich people: Yes, their houses are always bigger. They don't need to work for a few cents each day to buy bread, so their houses are understandably in nicer sections of town, set apart from the hubbub of factory and city life. They may have bigger yards, but then again they might not, and still be squeezed together to make more space for more rich people. The really really rich people get a spot all their own, with space for whatever they need.
Outer structure in cities tends to be the same, or very nearly the same. People can and do, however, change original structure, so unless it's a brand-new city, plan for that. Most people don't move the doorway around, however. This is where being able to recolor and/or custom pixel works in your favor, but it's not necessary.
YardsHouses can have small yards, big yards, no yards, fenced-in yards, open yards, but if they have yards you can always tell. There's never just houses placed willy-nilly on an open field. Houses with no yards tend to either: a) Not be houses at all (they're apartments), or b) They're inner-city dwellings with no room for a yard. And farm houses, while they may be randomly placed on a field, they're randomly placed on THEIR OWN LAND are generally separated by *something* (a road, a fence, a river, etc [if you look at farmland on an aerial view you'll see what I mean). If you have houses set randomly with no boundaries, you'd better have a good reason ("We don't believe in private property here.")
Other**THIS IS IMPORTANT!!** If you have a path on your map, that means that the grassy/wooded area it came from has been trampled enough times to create a clearly marked place to walk. That means that if you have long grass growing around, it shouldn't be on that path. If it is, it shouldn't just be on the path and nowhere else. Likewise, your entire map should NOT be covered in little bitty baby path squares that go nowhere.
If you have a big trade town, for the love of god don't put a town square right in the middle of the road! How are people supposed to get in and out with their goods?!
On Using the Canopy AutotileQuite frankly, I don't like it. I think (like most tiles in the RTP) it has potential, but the good folks behind RMXP just came a few coconuts short of a pina colada. Basically, the biggest issue with the tile is that it's square. What trees do [b]you[/u] know (besides hedges...) that are square?
I find that it *can* be used, in a pinch, for decent bushes, but if you're really gung-ho about using it on your map I find that there's really only one place for it: The bottom of the screen.

*Note: This is not a great map. It's used simply to illustrate another possible way to make a forest path, this time using the canopy autotile.
Now, I'm sure you've seen maps that use this autotile at the top of the map as well as the bottom. YES, it's possible to be used in that way, and if you've played Chrono Trigger, you've seen it at its best. This, however, is not its best. The RMXP RTP will never be anyone or anything's best. The issue with putting it at the top of the screen, put simply, is this: Given that you're looking at the map at a 3/4 angle, you should be able to see everything that that canopy is rooted in, ie tree trunks. However, in order to build an impressive (and decently realistic) forest, you need lots of trees, placed in different spots. To do that, you need to use different layers, specifically here layers 2 and 3. If you're keeping track at home, you'll realise that that doesn't leave with you with a layer for that lovely, hideous autotile...
So you're left with not using tree trunks at all, and having quite honestly a ridiculous looking map, or using tree trunks in straight lines not touching each other so that they're all on layer 2. :/
I've found it best simply not to use that tile at all, but I will admit that it's damned helpful. It marks the boundaries of the map, and it keeps the player from exploring too far into unmapped territory. Now if it wasn't so square...