Flower or Herb: Lily. It means purity.
Colors: Dark blue. I don't have a "reason" for this, other than many of the paintings done picture her in a dark blue cloak.
Animal: A lamb. According to http://www.houseofnames.com, a lamb symbolizes patience under suffering. How much more suffering can there be then watching your child cruixified? In addition, there are references to Jesus being the "Lamb of God" (Rev. 5:11-12).
Stone or Gem: Turquoise. According to the Illustrated Book of Crystals, turquoise unites the energy of the Earth and the Sky.