Bathrooms
Bathrooms come in three varieties: powder room (a half bath), the master bath, and the standard bath. The main distinguishing think between then is who uses them, rather than specific design. The powder room is used on a main floor when there are no other bathrooms on that floor, or at least no other with the common area realm (see Intimacy gradient). The master bath is accessible only from the master bedroom, and standard baths serve one or more bedrooms, as well as potentially the common area.
When laying out bathrooms, consider where the hot water will come from because if you keep the pipes short, you will save install cost, save water and energy, and hot water will arrive faster. Knowing where the kitchen is, it's time to start thinking about where the hot water source will go (see Utilities) and then you know where the bathrooms will be relative to everything else. Often bathrooms are put next to each other, or next to a kitchen or laundry room because this generally keeps the pipes shorter, but if you're going to do a home-run system (see the hot-water section), then clustering isn't as important as absolute distance since each fixture will get its own pipe. This is also a good time to start thinking about where laundry will be and try to put it near the kitchen, or heavily used bathroom as well.
If there is a bathroom where hot water won't be heavily used, for example a powder room, being far away from the hot water source isn't nearly as much of a problem as a bathroom that's used many times a day. Unfortunately, the one bathroom that tends to be isolated is the master bath because its part of the master bedroom, yet you can often keep it close, for example by putting it between the master bedroom and other bedrooms.
Bathrooms need a lot of light, yet they are often shoved to the north side and given only one window so that you have to turn on the lights, even on a sunny day to see in the mirror. Put them facing east to get good morning light, or on the south, or even the west, and don't worry so much about them getting warm: the bathroom can be the warmest room in the house, because its the one your guaranteed to be spending time naked in. If you can't find a way to get windows on two sides, look to put in a skylight. If the bathroom can only have one window, a second best option is to try to keep the distance from that window short--although that admittedly is often difficult since bathrooms have a tendency to be long and skinny. The one window often ends up either on a tub or shower wall, and this often leads to mold and rot, because water sits on the sill area. If the window ends up in the tub/shower, particularly on the side wall where shower water will hit it, consider a higher sill (say 4'6" off the floor or higher), and make sure the sill is sloped enough so the water runs off. A window in the rear (ie away from the shower head) is not nearly as much a problem.
The bathroom that serves the common area is the most challenging to locate: if it faces to directly to the common area people (Americans anyhow) are often embarrassed to use it, but if its too far away then its both hard to find and guests have to cross across into your private space. The ideal location is where the door is just slightly out of sight, but no more than a few feet from the common area. In addition to not wanting to be seen going in and out of the bathroom, people don't to be heard either, so if it can't be sound-insulated enough, consider an exhaust fan that is just a little bit noisy.
Most couple want their own bathroom, and so the master bath is typically located within the master bedroom, but can also be located at the entrance to the master bedroom if you want the option of occasionally sharing it. Ideally the master bathroom is located adjacent to a closet/dressing room, and potentially the two are designed as one, although consider that bathrooms have special ventilation requirements due to high moisture content, so keeping them isolated can simplify ventilation design. Most couple prefer having their own sink, but many also have no problem sharing. Many couples want their own separate sinks, and while this does make the room a bit bigger than the minimum (adding typically 6SF of counter, and 6SF of floor space), it also allows a couple to use the space simultaneously.
The space issue is especially acute in the master bathroom. Bathing need not be just a mechanical exercise; it can be therapeutic and enjoyable as well. A small cramped bathroom doesn't feel right, but then neither does an excessively spacious one. There needs to be enough room for both people to move around freely and places to put your clothes while your bathing without having to step on them.
Alternative bath arrangements: Typically a bathroom is one room, but it need not be. In many motels the sink is located in a alcove and isn't private, and the bathroom contains only the toilet and shower. Some bathrooms are one room, but the toilet is further separated by a door. You can also make each fixture its own room if you'd like: one for the toilet, one for the shower and one for the sink (where maybe the sink is just in an alcove). The advantage of separating bath fixtures into separate private areas is that it allows more people to use one bathroom at once, and hence allows you to reduce the number of bathrooms in the house.
Bath fixtures: In general, the sink should be closet to the door, and the toilet furthest as that is what most people find to be a comfortable arrangement. Try to keep fixtures from mounting to exterior walls so that you can keep plumbing out of those walls2, otherwise the warm water gets quite cold in the winter, and the cold water gets hot in the summer.
While a shower can have a smaller footprint than a tub (9SF versus 12.5SF), you will rarely save space by using a shower instead of a tub, and because showers tend to be wider than tubs they can be harder to fit. You can fit a shower in 30"x48" (10SF), and you can probably shrink it a bit further to 30"x42", but it gets progressively hard to move around in them.
Few people use a tub, and they're not the most convenient shower because you have to step over the edge, but for therapeutic uses, a tub is wonderful. An alternative it to only put in a shower, and use the extra space for a sauna instead. Energy wise, all the escaped heat from the sauna ends up in the house, while a good chunk of the heat from a tub ends up down the drain. Those huge jet tubs sell houses, but mostly end up collecting dust.
Under-counter mount sinks make it much easier to keep the counter clean, and especially help prevent mold problems around the faucets. Tile counters are pretty, but the grout around the sink is very prone to mold. Epoxy grout helps this a lot, but doesn't eliminate totally. Tile showers have the same problem: if you use tile, you need to squeegee it regularly. Even epoxy grout will grow a little mold. No matter what fixtures and counters you pick, consider the difficulty in cleaning and the possibility of mold.
Bath fans need to be quiet and go off on their own or they don't get used. In a tight house, it is critical they get used. If the windows fog up or have condensation, you've got too much moisture in the air. The one exception is in a slightly-to-public powder room--there the fan should be not the quietest one.
When designing the bathroom don't forget about the TP holder and towel bars or you're likely find you didn't leave space for them. Make sure there is storage room for spare towels, and whatever toiletries and cleaning products you have. If there isn't room for a closet or cabinet for these, some of them can go in the vanity, you can use the old style medicine cabinet/mirror combo that set in the wall (but beware of plumbing/electrical conflicts), and you can store stuff up high, for example above the toilet. While working to keep the size down, also consider just a little extra floor space so you're not stepping on your clothes as you step out of the shower. A small bathroom won't stay small if it's not very useable.1
Examples
Each of the above layouts are either very common, or are variations on a common layout, and their main feature is that they are quite small, but still reasonably functional. Each can be rotated and flipped, and in some cases the doors can move. Some of these require the use of a pocket door, and most of the rest will work better with one because it frees up the floor space where the door swings. In most of them the fixtures are where they need to be, but in some case they also can be swapped around.
The main flaw with all but #7 is that they have no storage other than the sink vanity, and the problem with #7 is that it really should have a pocket door to avoid door conflicts with the closet. Example #4 can easily have storage, but again it would end up behind the bathroom door unless the door is converted to a pocket door and if a closet were put there you would lose the only open wall space to put a towel bar. Example #3 could have a sizable closet if the door were moved to the left-hand wall (ie by the sink), but again the two doors would clash unless the bathroom door were a pocket door. Storage can also be right outside the bathroom, and many times this is easier than putting it in the bathroom: it just depends on where the leftover space ends up.
Of these example, the only one where the window will end up in the tub is #2, although depending on how the room is oriented, it could end up there in other layouts also.
In each of the layout with tubs, a shower of the same dimensions can be substituted for the tub. If you need to make it a bit smaller the shower can then be shrunk by 6-12"
Each of these layouts can be improved by making them slightly larger: they are shown smaller here because its easy the make things large, and hard to make them small. Note that a common theme in most of these layouts is that the door leads to what is essentially a hallway with fixtures on either side.
Double sink layouts are more difficult than single sink ones, if for no other reason there is no long history of design that's been polished over the years. The examples at right are derived from the single sink layouts, where the common theme is that the door leads to a "hall" and the fixtures surround that flow space. As with the single sink layouts, these are quite small, and also lack a closet. If you add another 10-20SF, you get a space for a closet and make it easier for two to move about in the room.
Notes
1: Obviously compared to the third world or living on the streets, these are trifling considerations, yet its pretty clear that there is a "reasonable" minimum that trades off human desires with the larger goal of being sustainable--at least that's what I'm shooting for here.
2: If you have a "utility layer", then this consideration doesn't matter. A utility layer is an un-insulated section of wall that the plumbing and electric run in.