I should have framed my question in the context of this semester being the worst (life-wife) I have had since starting back to college. I have had a death in the family, financial trouble, and have recently been diagnosed with severe migraine headaches (cluster headaches). I have never had to take medication before, and it is often as bad as the headaches themselves. I realize the semester is only half-over, but I’m a worrier by nature. Bottom line - as I should have posed before - if I do end up having a bad semester academically, will that do irreparable harm to my chances of getting into medical school? I do not plan to apply until May 07 for the 08 entering class, so I can always take some extra science in the fall to show my committment and boost my GPA a bit. Sorry for the venting, but I needed to do it. Any advice - good, bad, or otherwise - would be greatly appreciated. This site has been a great help to me.
Yes, failing a course will hurt your chances. Re-taking it and performing very well, plus your explanation of your difficult health and family situation can allow you to recover from the blow in many schools. I would also suggest you RIGHT NOW talk to the instructor, the department head, and the dean to see if you can get permission to withdraw with a W instead of a WF because of your health and family situation. Often exceptions can be made in these cases if you ask nicely and explain your situation.
I agree with Kasia that it’s important to try to figure out exactly what’s getting in your way in your class. I would go further and say try to find ONE THING you can change to improve your performance.
I would also suggest (even though I know you’re very busy) you be VERY INVOLVED in the decisions about the treatment for your headaches, and perhaps seek a second opinion. There are lots of different treatments for migraine and cluster headache, and there may be something that will work for you but won’t knock you down the way your current medication does. Unfortunately, one of the preventive strategies (eating and sleeping VERY regularly) is very hard when you’re in school, studying, and stressed. But it can make a difference, so try to squeeze something in.
Flunking one course does not have to keep you out of med school, even though it doesn’t really help you. Besides, there’s a lot you can still do to prevent this problem from occurring. Get to it! 
Migraines and clusters are not the same thing. I’ll take a migraine anyday over these godforsaken clusters.
Withdraw, withdraw, withdraw. A bad grade as a traditional undergrad is recoverable but as a nontrad it like shooting yourself in the foot at the beginning of a marathon. Sure, you can finish but it will be very slow and very painful.
Better to explain a W than a C or D. W’s create questions but a bad grade let’s them know you couldn’t hack it. At least with a W there’s room for “what happened?”. C or D…“we know what happened, you couldn’t hack it”.
None of this is cast in stone but this was the advice I received from an adcom during the summer when I was going thru my craziness. Might be different where you apply but better a W that doesn’t affect GPA than a C or D that will crush your GPA.