Flowers are a common centerpiece idea, and come in a variety of forms. Consider using potted plants instead of cut flowers. These can then be given to your guests or planted to commemorate the wedding. If using cut flowers, get them from local growers, and look for organic and sustainable growers. Inquire about pesticide use. Stay away from true wildflowers, using only wildflowers that have been cultivated. You (or a friend with garden space) might even be able to grow your own cut flowers, with a little planning. After the wedding, the flowers (cut or potted) would be much appreciated at a local nursing home, hospital, or other institutional setting.
Candles make excellent centerpieces, but consider the materials used. They can often use petro-chemicals and other polluting, non-renewable resources. Soy based or beeswax candles might make a good alternative to your typical candle. You may even put custom labels on the holders for a personalized effect. Soy candles are a highly renewable resource (soy!), burn cleaner than typical candles, are bio-degradable and are versatile. Don't forget to shop around and see if there is a local seller with whom you could work to cut down on fuel usage in shipping.
Bamboo is an attractive and renewable alternative to many of the materials commonly used for favors (such as wood or plastic based candle holders. If you are interested in using candles for favors or as centerpieces, consider bamboo. For the symbolically inclined, an additional benefit to using bamboo is that it symbolizes good fortune. Living bamboo shoots are also an alternative to cut flowers as centerpieces or even favors.