If you haven't installed the hardwood flooring yet, consider alternating the direction of the boards from room to room. This will give your home a continuous flow of hardwood while at the same time providing clear transitions. For example, define the living room with boards that are lined up from north to south, then lay the boards in an east-west direction for the adjoining dining room. You can also use shorter boards to transition into a new room.
Use thin strips of wood to define transitions from room to room. These "finishing pieces" are often used to finish off the raw edge of a hardwood floor where the ends of the boards line up against a wall, or as border pieces, but they can also be used as transition pieces. Just lay the thin strips of wood across a space to define where one room ends and the other begins, incorporating it into the design as you or your contractor installs the floor.
Continuous hardwood flooring doesn't have to mean using the same type of wood throughout the house. Consider changing up your wood depending on the room. Some hardwoods are more durable than others. Brazilian Cherry, for example, is one of the hardest types of wood, and that makes it extremely durable -- a good choice for high-traffic areas. In addition, because each type of wood varies in color and grain, the visual differences will mark the transition from room to room.
Area rugs offer perhaps the easiest way to create room-to-room transitions when you have continuous hardwood flooring. The rugs bring color to the space and show off nicely against the wood floors. Simply lay the rug in the space where the transition occurs. Or use area rugs to anchor furniture arrangements. This is especially effective if you have a large, open area with continuous hardwood flooring and several different gathering spaces, as the rugs will differentiate each space.