First of all, address moisture and mold problems. Any old home is likely to have excessive mold in the attic or crawlspace from rain or water leakage. Ask a professional to help you correct any of these issues, because mold is a known health hazard. You'll need to make roofing repairs and foundation repairs in the process, to get the house in sound condition.
Carefully go over energy needs for the house. You'll need energy-efficient windows -- or tighten up all the spaces around the existing ones -- and new insulation in exterior walls and attic areas. Living in an old home doesn't mean ignoring a bad heating system or air leakage around baseboards, for example. To protect the home's livability and market value, it will need a modern heating and cooling system and a careful assessment of any drafts or waste of energy.
Preserve walls and window spaces. Decide whether to redo walls in existing board materials, for example, or add new drywall or plaster. Talk with a local historic preservationist, if possible. To keep the exterior as authentic as possible, you will want to keep window openings on the front facade with no changes in dimensions in most cases. You can, however, reduce or enlarge windows in other exterior walls for a remodel. Energy-efficient windows and framework are required in all instances, however.
Look at all woodwork and flooring to save what you can. While you don't want a sagging bathroom floor with warped boards, you might be able to save door and window facings and part of the flooring. Keep any unique kitchen cabinets or storage spaces, if possible, by planning a kitchen remodel to incorporate them. Have a local artist paint flowers or roosters on white storage cabinets to create a warm, farmhouse feeling.
Old furniture and artwork will be important to the project. Try to purchase sofas, tables and a china cabinet, for example, that fit the home's original period. You can use a couple of leather sofas in the family room, but include an old lamp and a table from a century ago. Buy an old light fixture and rewire it, along with any old lamps, to ensure they are safe to use. Use headboards in some of the bedrooms that fit the home's construction era, but incorporate other pieces that would work in modern homes. You can hide media equipment behind closed cabinet doors when it's not in use.