Hot water heaters and furnaces often end up in either the basement or garage because space wasn't set aside for them, and in most cases there is a significant energy cost because the basement and garage are not in the conditioned space.  However, whether this is the case or not depends on the climate, and somewhat on what the equipment is.  How much space you need and where the equipment is installed will also depend on the specific devices installed, so you need to at least make a preliminary decision about what you're using at this point (see the heating and the hot-water sections to help make that choice).

The hot water source is best located equidistant from the various plumbing fixtures, or at least equidistant from the most used ones.  On the flip side of this, if you design so that the rooms with hot-water plumbing in them are as close as possible, this also reduces the pipe length.  Even with an on-demand unit, its always challenging to find space for hot-water on the main floor, so it often ends up in the basement, attic or garage.  In other than hot or very mild climates, the hot-water unit should be inside the heated envelope, hence you may need to build a insulated closet for the unit.  However if you're using a heat pump water heater, they usually go in unheated space (except that space much stay above 40F, and have an average temperature of at least 50F for the units to work).  In hot climates, you can put the heat-pump unit inside the envelope as long as you can deal with the cold it spits out all year and its noise level.

The attic is often ideal for a solar hot-water tank since the collector is generally on the roof, but it's nearly as good in an insulated basement space provided you insulate the pipe from the collector really well.  The advantage of the basement space for colder climates is that you will likely have temperature stratification in the closet, so its more heat will move up than moves down, but of course it will do this in the summer also, so it may be better to just insulate the entire space.  The garage is generally a bad place for a hot-water tank, unless the average temperature in there is warmer than the average temperature of the house, OR it will take more cooling energy to eliminate the escaped heat than the extra energy that is lost due to a cooler temperature in the garage.

Wherever the hot-water unit ends up, keep the pipes out of exterior walls, and if you do have to put a pipe in an exterior wall keep then as close to the inside as possible.

The location of heating systems is less critical, although if they're not somewhat centrally located care must be taken to make sure the more distant rooms get the correct amount of heat.  This is especially true for forced air and fan-coil units.  Water tends to hold heat better, so radiators or wall mounted fan-coils are less sensitive to location.  It is however, important to keep any ducts or pipes within the heated space as much as possible, since insulating them well enough when they're not in the heated space tends to be quite difficult.  If you're using a ductless mini-split you won't need to find space for the unit at all, but you then have to consider how the heat will be distributed.  If there is to be only one unit, it will typically go in the common area, and just letting the bedrooms be cooler. Since the units are noisy, a second unit would likely go into some common hall near a bathroom rather than in a bedroom. In this case it might be better to go with a ducted system, in which case the air handler will need to be centrally located.

Whole house ventilation systems are also generally best if centrally located, and although some  systems are quite small, the ones with multiple small diameter pipes are not so small.  Unless you're using the ventilation system for heating, the location of the ducts is less critical since the air isn't heated, but still its best to keep them in the heated space.

Combustion appliances have specific ventilation requirements that must be met, so make sure those can be provided.  Likewise heat-pump water heaters also have very specific requirement--they need a lot of air that never gets very cold.

All the utilities don't have to be in the same space--for example, a hot water tank might be in an insulated space in the basement, and HRV in the upper part of a closet, and a mini-split heat pump mounted in the wall.  Often the ventilation system is combined with the heating system, but this is not required, so they can be installed in separate locations.

If you built a closet for utilities in the basement or attic make sure there is a reasonable way to both service the equipment and also replace it.  The one limitation of closets for utilities in super-insulated homes is that its often challenging to insulate the closet to the same level as the rest of the house.