Ed Lewis investigated and won a Nobel Prize in 1995 for discovering a small set of genes that affect different body parts (Hox or Homeobox). They act like ‘architects of the body.’ Mutations in these can cause ‘dramatic’ changes. Many experiments have been performed on fruit flies (Drosophila), where poisons and radiation induced mutations.
The problem is that they are always harmful. PBS 2 showed an extra pair of wings on a fly, but failed to mention that they were a hindrance to flying because there are no accompanying muscles. Both these flies would be eliminated by natural selection.
Again, citation for the 99.9% number.