I know of two labels (well these pop into my mind anyways ):
Somnia managed by Bluetech, the covers are made by hand (recycle paper), sawn together and colours pressed with soy ink... and the end result is really nice and unique!
http://www.altar-records.com/"</a>'>Altar Records managed by DJ Zen, not really sure how its eco-friendly... but I seem to remember its recycle paper, he will probably clarify him self I hope!
ED:
But there must be more...