For the last century fish have carried increasing levels of mercury and other contaminants. Carnivorous fish have more, because many toxins bio-accumulate. Equatorial fish have more, because there are more people and hence more pollution around the midsection of the planet. Interestingly, since the economy took a dive a few years back, the mercury levels in fish have declined. Some say that it is because there is less coal being burned in China. Most environmental mercury comes from coal smog. All this is debatable, but the fact that there is mercury in fish, and that mercury is bad for people, especially people's brains, is very well documented.
So what do I do? I eat fish 1-2 times a week, and supplement fish oil, ideally every day, though I often fall short of that goal. I choose fish that are less likely to have a high mercury load---less carnivorous fish, smaller fish, more northern fish, instead of tuna from near the equator. I supplement zinc, because being replete for good metals reduces one's absorption of bad metals when introduced. And I support my liver's detoxification mechanisms in many ways, not the least of which is eating sulfur rich foods like cilantro and garlic. I don't know exactly what balance will be right for you, but it is worth being conscious of the toxic challenges that may be in your food, and acting intentionally about it.
Here is a site where you can find out how much of what is in the fish you eat:
Edit 11/28/11: I just heard that fish have high enough selenium levels to bind up most of the mercury that they ingest, and possible render the majority of it non-absorbable to us. I have not confirmed this yet, but it brings up the question: would repletion for selenium benefit humans with regard to avoiding mercury toxicity? I do know that most humans are deficient in selenium. And I also know that selenium is a key cofactor in the activation of thyroid hormone; if you don't have enough selenium, you will feel tired. So it's worth considering both selenium and zinc as nutrients to bulk up on if you want to eat fish. More updates as I learn more!