Well, let's see….the FDA never approved thalidomide for morning sickness, but millions of doses were distributed as part of a clinical testing program, according to Wikipedia. My mother was given thalidomide when she was pregnant, and never told that it had not received FDA approval. (Luckily, she never bothered to take it, as her morning sickness was pretty mild.)
The FDA did approve Vioxx, and Lipitor, and a truckload of antidepressants, all of which can have very serious side effects that were not initially disclosed. The antidepressants have been declared by the Cochrane Review as being no more effective than a placebo for mild-to-moderate depression, which is the majority of the cases where antidepressants are prescribed.
Lipitor has several class-action lawsuits pending. It has recently been announced ("announced" almost silently--it never made mainstream news) that it is linked with high risk of diabetes in middle-aged and older women, kidney failure, musculo-skeletal problems, liver problems, and memory problems.
Antidepressants can cause long-term serious problems, including increased risk of stroke, thicker arteries, miscarriage, birth defects, sudden cardiac arrest in women--and, of all things, antidepressant use may be linked with autism. There are no long-term studies, because they haven't been in common use for that long, and there are very, very few unbiased studies.
The flu shot is FDA-approved, even though efficacy is very poor, and people have been permanently damaged by it.
The Hep B shot is approved for ALL infants, for the day of birth, even though it, too, has some serious side effects in a small subgroup, efficacy is not long-lasting, and most infants are not at risk during their first year of life.
Gardasil was fast-tracked to FDA approval, and has the highest rate ever of reported severe adverse reactions. Merck never bothered to tell the public that efficacy is 4-5 years.
The chicken pox vaccine was FDA-approved, NOT because chicken pox is inherently a dangerous disease, but becasue it is so inconvenient for working parents. But FDA approval of a pediatric vaccine always leads to that vaccine's becoming mandated--as it now is. We are only now learning of complications from the varicella vaccine--including the fact that older vaccinated children have a significantly higher rate of shingles than their unvaxed counterparts. Shingles is far more serious than chicken pox.
I'm sure there are more...