What causes "old smell" in a clean but older house?
Normally it's the things you can't see. 

Moisture building up behind walls or creeping up through micro-fractures in the foundation will cause mold and mildew to grow fairly quickly.

A fairly cheep way to prevent this is to use a powerful dehumidifier to really dry out offending spaces. 

Avoid carpet, as no matter how clean it is, will always harbor bacteria that can cause unpleasant odors.

Old insulation can also be a big source of a constant odor that, while to too offending, is incredibly pervasive.

And finally, mothballs. Some people used to use them as a "catch all" solution to pest problems, and used them so much that the very material of the home absorbed the smell, similar to the way homes that housed prolific tobacco users can smell for years after even with deep cleaning.