Room List
In addition to determining you needs based on your current house, you can also go thru a standard list of room, and fit your activities into them. The discussion here is more in terms of things to think about rather than specific recommendations, since the decisions about rooms are very personal.
While the main "green" reason for this exercise is in hopes of keeping the size down, there are budget reasons to do it also, especially given how frequently builders end up giving customers price estimates that are beyond their budget. A good way to avoid this is to involve the builder in the schematic (early) design phase as soon as the plan starts to coalesce: a good builder can suggest ways to keep the project in budget. Having done this exercise once, you can then repeat it with a finer toothed comb, simplifying the building or eliminating space that was of lower priority.
Most house's room list are built on some variation of the three beds, two baths, living and kitchen and although it often doesn't match what people need, these plans have proven to be fairly adaptable. When designing your house, think also about future owners: not just because of the environmental impact, but resale value. See more under adaptable reuse. When building your room list, consider combing uses that are not that common, for example a guest bedroom with some other activity as a way to keep the size of the house down.
Common area: The common area is all the space the entire family shares--kitchen, dining, living, family room, den, bonus room, away room, library, sitting room and so on. The activities here are cooking, eating, and socializing in various ways ranging from fairly quiet (reading, listening to quiet music) to fairly noisy (TV, games, entertaining guests). In the degenerate case, the common area might just be a kitchen and an eating space, but more typically will include a room for social activity as well, and may include two social areas allowing for a separation of noise levels.
Traditionally the common area consisted of a separate kitchen and living room, and in the higher end homes a separate dining room. In this more formal arrangement, guests were often banned from the kitchen. Even if there was a dining room, sometimes the kitchen had an informal eating space (usually called a "breakfast nook") as well. Now, these are usually done with one " great room", and since this decision constrains layout a bit, you want try to decide now how much separation you want. (if you're undecided, read more in the common area section).
Decide whether you want one eating space or two, and how much space you want for each. A breakfast nook can be somewhat spacious (50SF or more), or it can be quite small (15SF) depending on how many people it can accommodate. In the great room design, a dining area need only be big enough to accommodate the typical number of family members and then expand into the living area for special occasions--although obviously this only works if the furniture is relatively easy to move. If there is an alcove off the dining room, you can let the dining room expand into that space as well. Alternatively you end up with a space large enough for holiday gathering, most of which sits unused most of the year. By being creative you can make use of this space the rest of the year, even if you opt for a separate dining room. At this point design in everything you want, but consider which are critical and which you can live without. As you start assembling the pieces, some things will fit easily, and others will tend to force the whole building to be a bit larger.
The remainder of the common area is for social gathering-either quite or noisy. Because the great room design provided no sound isolation, sometimes the social gathering space is in two parts, one of which is walled off separately so as to contain sound. The biggest issue here is the TV, which dominates the room more than the most incessant chatterbox in that it literally never stops talking. Even with the sound off, the problem is that we are preprogrammed to focus on movement in our field of vision, and television takes advantage of this by presenting a constantly changing view. Because of this, where ever you place the TV, it will generally prevent the room from being used for anything else. If there are children in the house, this is the time to make space for them or a retreat for the adults (see "children's place"). It isn't necessarily the only reason for a mismatch between quiet and noisy activities, but its the most common one because in many households it only many hours a day.
The first question is to decide whether there is enough of a mismatch to require a separate room. In some households the TV is rarely on, and in others when its on, everyone is watching it, yet in others there are multiple TVs because people are watching different things. If there is only one person who wants quiet, than consider "a place of your own", and make that quiet. If the common area is generally quiet except on regular occasions (for example a one a week card game), an existing space like a bedroom, guest bedroom or home office can provide temporary refuge for the occupant seeking quiet. If none of these solutions work, you will need a separate space. Next decide whether this separate space will contain the noise (ie the rest of common area is generally quiet), or the separate space will be the quiet space. In many families the answer is obvious, but sometimes this will require careful negotiation.
Most people spend the majority of their day in the common area, so it makes sense to allocate the majority of your space there. Its not unreasonable to size this area carefully to what you want, particularly the kitchen, and let the other areas, such as bedroom potentially end up a little smaller.
Bedrooms: One, two, three or more? Obviously it depends on the size of your family, but what happens when the children move out? Spare bedrooms turn into craft spaces, guest rooms, home offices etc, but that often means living without such spaces while the children are growing up. If there is any chance of an elderly family member living there, then this could also be one of the future uses. Children may each need separate bedrooms, or a larger room might also work. Bunk beds are often a hit with children, and one very space efficient option is give each child a bunk-type bed, only where instead of a 2nd bed below, there is a desk. You also need to decide if you want a place to put up out of town guests, and if so will it be shared with some other activity, like someone's own space, or a home office, or even a hide-away bed in the common area.
Bathrooms: Before 1900, most houses had little indoor plumbing and instead went outside or used chamber pots. If there is one luxury that the industrial world has brought that's both universally loved and also taken for granted, its indoor plumbing, hence its no surprise that very high end houses tend to have quite a few bathrooms. Although these houses likely have far more bathrooms than necessary, anyone who has lived in a house with only one can attest that too few results in frustrating conflicts.2 As with every other "just the right size" exercise, the key is finding the right number for your situation, which is related to the number of occupants, or alternatively to the number of bedrooms, which reflects the number of possible occupants.
From a size perspective, most bathrooms have very small footprints, often only 40-50SF, and a powder room can fit into 15SF, so an extra bathroom doesn't generally make the building grow much. However, bathrooms are typically the second most expensive rooms in the house (after kitchens) due plumbing, cabinets, tile, counters etc, so the limiting factor on number of bathrooms is often budget.
In general, every floor should have a bathroom of some sort--depending on the rooms, a powder room might be all that is needed. One of these should be easily accessible from the common area (see bathroom layout). If there is a bedroom somewhat near the main floor, its bathroom can also serve the common area. A upper floor that doesn't have bedrooms can omit a bathroom, but then using it as a backup bedroom become a problem, especially, for example, older people who have to get up at night frequently end up sleeping in that space. Most couples want their own bathroom, and then there is at least one bathroom for all the other bedrooms. Most homes will want at least 1-1/2 baths, and few will want more than 2-1/2. Since the sink and toilet are used far more than a bath/shower, a power room (1/2 bath) can alleviate congestion with a small footprint.
Children's Place: Children are both energetic and noisy, so you need to provide a place where they can do that without disturbing everyone else. Any place that children frequent effectively becomes their space, because it is their nature to be that way, and some families find this acceptable. If this isn't acceptable, put a place for them on your list.
Place of your own: Many adults want some place to retreat from the hubbub of the rest of the family, often to read or pursue a hobby. Often the space need not be large, and depending on the person it doesn't always have to be a separate room, but it does need to be private enough that whatever book or project you're working on will be left undisturbed by everyone else. An alcove off the hallway, and alcove in the bedroom or even off the living room can all work, but of course any space that isn't physically separate runs the risk of having conflicts.
Another alternative is to provide a generic quiet room shared by all. This does better than an alcove at providing quiet, but does not really provide the feeling of your own space unless each family member who uses it has their own corner.
Storage: Storage is usually an afterthought, often occupying leftover spaces, and as a result there is often too little of it1. Take an inventory of all the things you access regularly and make sure there are place for them. Some common items are: kitchen garbage, recycle and compost, canvas bags, plastic bags and food; the vacuum, brooms and other cleaning supplies; shoes, coats, umbrellas; office supplies, bills to be paid, checkbooks. When designing kitchen cabinets, make space for a reasonable amount of dishes, pots and pans, but no more. Finally leave your self a lot of extra storage, both easily accessible from indoors (for things like holiday supplies and other rarely accessed things) and from outdoors for garden tools etc. The attic and basement are often ideal places to store things: but they spaces are only good for items that aren't frequently accessed. Also, if the house is going to be slab-on-grade with a truss roof, you an end up with neither, so if you want that sort of space you need to plan for it now.
While is has been argued that basement are no longer needed (they were originally used as root cellars), in an urban setting where land is expensive, a basement is a way to build space and keep the building footprint small. The alternative is extra garage space or a shed out back. Otherwise there is no place to put bicycles, camping gear etc.
There are three storage needs that are often overlooked: pantry space, recycling, and a place for all the miscellaneous paper.
Every house has the inevitable piles of paper that accumulate: magazines, newspaper, bills, requests from charities, invitations, coupons to local merchants, bank statements, tickets, community notices, outgoing mail, and even an occasional letter or card. Many households end up with this paper scattered in multiple places: kitchen counters, dining tables, table in the entry, stairways etc. because there is not real place for it. With the increasing paperless economy, maybe you won't need a space for this, but until then, consider building a place for it.
Pantry space is also often short, and designing a large pantry and having it not take up a lot of space is a challenge. The most efficient use of space is as cabinets no more than about 18" deep, rather than a closet of some sort. They key is that you need to be able to see and reach the back. A door with a rack that holds things will make space much more accessible, or alternatively you can put shelves on full extension drawer glides and that will allow you to make the cabinet up to 30" deep (any longer than 28" and glides start getting very expensive).
Recycling can take up a ton of space, and unless you want to carry it all out to the garage or where ever you store it before it goes away, you will want enough convenient recycle storage to avoid going outside all the time. It doesn't necessarily need to be in the kitchen, but it does need to be semi-convenient, otherwise it will end up collecting on the kitchen counter until someone finally takes it away.
Walk in Closet/Dressing Room: Walk in closets are not efficient ways to store things since often 1/2 the space is walkway (For example shelves 15" deep on both sides and a 30" walkway in-between). However if part of the space is used as a dressing room, then that equivalent space can be left out of the bedroom, or in any case making the walkway space in the closet more useful.
Flow/Halls: you need to be able to get from room to room, and there are two solutions to do that: pass thru each room, or use a hall. While passing thru would seem to save hallway space, in fact you will have to keep pretty much the same amount of space in the room open, otherwise you can't pass thru. However, that flow space could be the same space as is required of that room anyhow.
While flow-thru can work well in the various common areas, obviously this doesn't work for private areas. Rather than having these hallways be only space you pass thru, consider thickening them so they become rooms in their own right. In this thicken space you can put bookcases, a window seat or other sitting area, a small desk or a mail sorting area. It can be a great way to make small quiet, private spaces and use very few extra square feet.
Stairs: at this point, the question really is: how many floor will you have? Obviously if you're going to have multiple floors, then you have to fit stairs in, although you can add a loft and only use a ladder to access it. If you're on the fence about number of floors, consider that stairs take up as least as much space as a small bathroom, and that space is removed from both floors.
Utilities: Utilities usually end up in the basement or garage, because there is no other place for them. Depending on your climate this may or may not be good thing (more in the utility layout section). If it makes sense to have them there in your climate, then problem solved. Everyone else will have to find space for them either inside the envelope or by building an insulated space somewhere.
How much space you need will depend on what devices you pick, so you need to decide what they are so you know how much space to allocate for them. Heating systems are described in the HVAC section, and hot-water systems are in the hot-water section.
Notes
1. it could be argued that most Americans have too much junk, but even with this alleviated, many houses would still have too little storage.
2: this probably sounds a bit like a spoiled American, given the number of people worldwide that live with much worse situations, but I'd argue that bathrooms are generally desirable by most cultures and for the cultures where they're not, bathrooms provide a huge public health benefit.