Water and Septic
Send out a sample of well water to your country cooperative extension to test it for chemicals and bacteria.
Make sure that the well cover is tightly sealed but there is still access to the pump.
Check the sump pump by pouring water on it, to see if it turns on automatically.
Look around your septic tank/field for soggy ground or overly lush vegetation, which could mean the tank is full or failing.

Heating
Take a flashlight into the furnace flue and look for a buildup of soot or rust. Tap on it to see what falls; rust is a sign of condensation, which is cause by an inefficient furnace. Have a pro service the system regardless of what you find.
Make a solution of dishwashing soap and water, then brush it on ductwork joints-wherever there are leaks you'll see bubbles in the soap.
Check registers and vents for loose or missing covers and screws.
Check around radiators for leaks, or damaged floors, which could be a sign of a leak or an incorrect pitch toward the return.
Look for overall deterioration, rust, loose parts, and other signs of a failing system.

Download a printable version of the entire Yearly Inspection Checklist here.

See some of the crazy things house inspectors find in Home Inspection Nightmares.
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