I do like that idea! Did a quick search and came up with this:
"River rocks, with their smooth sides and hefty weight, are ideal for plant markers. Use a permanent marker or an etching tool to write each plant specimen's name on a rock, spray the writing with acrylic sealer and tuck the rock close to the plant."
Another site also mentioned using acrylic paint for painting on rocks, and then sealing with clear acrylic spray.
No idea how well this would work, but it sounds good!