The thing that really works for me is the old-fashioned vinegar jar routine -- works like a charm.
I use old food jars (well washed, of course). Put about a tablespoon of vinegar in the bottom; add about 1/4 teaspoon of liquid dish detergent; fill the jar about 1/4 full with water and shake to make bubbles. Punch a few holes in the lid of the jar and put it on.
The fruit-flies get in through the holes (they love vinegar, for some reason) and then get caught in the soap bubbles if they don't drown first. Shake it a little once in awhile to refresh the bubbles.
When you've got a lot of dead ones, you can just dump the whole thing down the drain, rinse the jar, and start again.
And here we go for 2009 . . . Onward and Downward . . .