Cotton batts or formaldehyde-free fiberglass batts work well to insulate your floor, from the crawl space below.
Emissions from insulation in ventilated crawl spaces below the floor are not likely to get into your house, but formaldehyde-free products are preferable.
Choosing an insulation material
Fiberglass batts are the standard, and encapsulated fiberglass batts would reduce your exposure to itchy fibers. Working your way around plumbing or blocking would be tricky, however.
Cotton batts cost a bit more than fiberglass, but cotton batts are more user friendly during installation and whenever you need to access your crawl space. The borate treatment in cotton has virtually no impact on air quality, and no protective gear is needed for installation.
Another option is cellulose insulation, which typically requires professional installation in overhead applications, and would make access to plumbing more bothersome.
For more information:
GreenHomeGuide's "Choosing the Right Insulation Delivers Energy Savings" gives an overview of insulation materials.