- Phenanthrene derivatives are used as pain medications (morphine, codeine, oxycodone)
- Steranes are probably the most common hydrocarbons used in medicine, as all steroidal drugs have a sterane core with non-hydrocarbon functional groups
- Hydrocarbon carotenoids are often taken as a supplement, so they can be considered a consumer medicine
- Parrafin oil can be used as a laxative
These are the ones that came to my mind. Hydrocarbons aren't pervasive in medicine due to their toxicity and ability to cross the blood-brain barrier (in many cases).