You always have the option of going back to the basics?buying a bag of drywall mud and mixing your own spackle. This is the most cost-effective way and is also a very green approach. You'll use less packaging and fewer preservatives (but more elbow grease).
There are also prepared solutions available at green building specialty stores. The green equivalents of common products like spackle work great, as long as the product is maintained as per the directions on the package. (For example, don't let a product sit open in direct sunlight.)
Crawford's Free Spackling Paste is an eco-friendly spackle that comes in half-pint or quart sizes. The product is available from Ecohaus; you can order it by phone at 800-281-9785.