A durable shower pan is of utmost importance. If it fails, water can do serious damage to your house and repairs can be very expensive.
The first thing to do is find out what local building code requires-your options may be limited to the ones you mention. Various techniques and materials are accepted in different parts of the country, including PVC or CPE (chlorinated polyethylene) sheeting, copper and lead pans, and "hot mopping" with molten tar.
As you may have guessed, all of these methods pose environmental concerns. I welcome others' comments, but at this time I don't know of reliable alternative materials commonly in use.
It may be best to use one of the less sustainable but proven options, like PVC sheeting, while focusing on the finish as a location for incorporating sustainable materials. If you use an unproven alternative and the shower leaks, you will have to tear everything out and start over, generating waste and defeating your original goal of keeping the project green.
Recycled glass tile and reclaimed stone are excellent green finishing options. Because these materials are heavy and require more energy for transport, it's best to find a local source. GreenHomeGuide's stone and tile product directory includes many choices, and the Green Stone & Tile Know How articles provide product comparisons and other helpful information.
Select adhesives and sealants that are not only appropriate for the intended purpose but also contain minimal VOCs or other toxic materials. To stay green, use a tile adhesive like AFM Safecoat's 3-in-1 Adhesive, W.F. Taylor's Envirotec Adhesive, or CHAPCO's Safe-Set Adhesives.
For more information:
John Bridge Ceramic Tile Forum is a great resource for many types of tiling projects.
For more information about recycled content ceramic tile, read this guide to recycled content ceramic tile from Build It Green.