Since marijuana is still illegal recreationally at the national level, it's difficult to conduct the best type of research, control studies. Some state AMA chapters, California in particular, are supporting legalization of recreational marijuana specifically to help facility these types of future studies.
In regards to what we know about marijuana to date, studies have shown both health risks and health benefits. Benefits include helping suppress nausea and vomiting, especially during chemotherapy, treating pain and increasing appetite in those having a hard time keeping their weight up. Although studies have shown that marijuana can lower eye pressures that could lead to glaucoma, it doesn't work as well as current medications used for the same purpose.
But marijuana also has health risks. What's unknown is how it affects the lungs long term. It does contain both elements that seem to cut down on the risk of lung cancer and many elements that increase your chances of getting lung cancer. Teenagers who are heavy users of marijuana also ended up showing lower IQs later in life.
One big issue is impairment and driving. Right now, we have standards and testing methods to determine if someone is under the influence of alcohol when driving or operating heavy machinery. The same isn't true for marijuana. Both the health care and legal fields are trying to figure out the best testing methods and limits to determine if someone is driving under the influence of marijuana. This will probably take some time to not only come out with testing methods but to also have these methods work their way through the court system to see what holds up to current or future legal standards.