If you're worried that your fish supper is adding to problems of over-fishing then check out the Marine Conservation society's website. It's got a full and up-to-date list of fish not to eat. These are some examples taken from the website in August 2004. The society says that these are best avoided to help conserve fish stocks.
Atlantic salmon - wild caught
Tuna (unless it's dolphin-friendly caught with a pole and line or by trolling a jig)
There are more fish than that: Snook, a delicious game fish from south, like florida should not be kept. though delicious, their numbers have declined. Any fish with a bill, marlin, swordfish, etc is best to avoid. Eat bluefish, there are tons of them around.