The reality is that only about 5% of all medical practice recommendations have good quality evidence behind them, and perhaps another quarter have some evidence. The rest of medicine is practiced by "the seat of the pants" approach, or "the 15 years of experience" method. Clearly, this is not wrong when there is absence of evidence.
It is a fallacy, however, to confuse this absence of evidence with the evidence of absence of an association or an effect. What I mean by this is that in the former no one has bothered to generate the evidence, whereas in the latter there is evidence that does not support an association between the exposure and outcome. The latter is in fact evidence, while the former is absence of any evidence.
The distinction may be subtle, but is worth making. Take some of our environmental policies, for example. There are 80,000 potentially toxic chemicals on the market, including household cleaners, pesticides, etc., of which only 200 have been evaluated for toxicity by the government agencies. Does this represent the evidence of absence of any harm to human health? Of course not! This is a clear case of absence of evidence -- we have not deemed it fit to put resources into investigating the association between exposures to these chemicals and health. So to say that these chemicals are harmless would be a fallacy in the absence of a concerted effort to study them in the context of public's health.
Similarly, because our adverse drug reactions reporting system has traditionally been voluntary, the absence of reporting does not equal the absence of adverse events. Again, a classic situation of absence of evidence and NOT evidence of absence of these events.
So, given what I have just said, it is in fact difficult to practice evidence-based medicine or evidence-based public health. Unfortunately, even the evidence that exists is slow to wend its way into practice. As the RAND researchers demonstrated several years ago, the median penetration of evidence into practice is on the order of 50%, which is no better than a coin toss! So, we can certainly do better than that. When there is evidence. But, let's not be fooled: most of the time what we end up practicing is absence-of-evidence based medicine. Question your doctors closely to distinguish between the two, as this distinction is the key to rational decision making.