My opinions (for what they are worth):
-Atheism
-Should not be stigmatized. I think the stigma attached to this depends on how heavily religious the area is. More liberal areas even glorify this. Is NOT stigmatized in mass media.
-Homosexuality
- See atheism.
-Marijuana
-Jury is still out on whether this is all that harmful when used recreationally. Should definately not be stigmatized in regard to medicinal use. Should probably be legalized and regulated.
-Smoking
-Proven harmful. Should be stigmatized, as a public health measure.
-Gun ownership
-Should not be stigmatized (personal bias - I own 2 handguns). Currently is stigmatized in almost the direct opposite way of atheism and homosexuality (i.e. liberals don't like it)
-Mormonism
-ALL cults and high control groups should be stigmatized, as a public (emotional) health measure.
-Sex
-See homosexuality and atheism.
-Fetishes
-??? - Should not be public enough to be stigmatized.
-Tattoos
-Depends largely on quantity, quality, and location. I would personally stigmatize anything on the face, neck and/or hands (maybe even lower arms). Traditional locations on the shoulder, chest, back (not too sure about "tramp stamps", though), and (for the ladies) ankles, are fine by me. ANY tattoos indicating gang affiliation should be heavily stigmatized.
-Mental illness
-Should not be stigmatized, per se., so much as sympathized with and treated to the extent possible. Where a mental illness can render one violent, there is a certain understandable mild stigma for self-protection.