What are the potential side effects of medication?

Can be anything. Medications can cause side effects form the minor ones (tiredness, aches); moderate ones (nausea, vomitting, diarrhea, rash); severe ones (allergic reactions, kidney damage, liver damage, blood problems); and finally life-threatening (anaphylaxis, heart damage, lung damge). Always check with your physician and pharamcist to go over side-effects and potential interactions among your presciptions.
A broad question. All medicines including "natural" substances have risks and benefits. When considering a course of action you also need to consider the risks and benefits of not doing anything. The handouts from pharmacies list side effects seen in the trials the fda used to approve the medicine. Clinical experience later reveals a more accurate picture of what is common and uncommon. Work with your doctor.