When shooting landscape and cityscape photos that include water, I prefer to give the surface of the water a smooth, "whispy" texture. I usually find this effect to be much more attractive, and perhaps calming, than having the water surface appear choppy. This is achieved with a long exposure.
Here is an example of a photo where the surface of the water is choppy. The photo was shot hand-held at 1/30 sec. The relatively fast shutter speed did a good job of freezing the motion of the water.
And now here is another shot of the NYC skyline with a smooth water texture:
As you can see from my settings, the exposure time for this image was much longer than the first one. I set my camera on a tripod, selected a 30 second shutter speed and fired the shot. During the time that the camera was exposing, a great deal of water flowed past, creating a very smooth texture on its surface. You can try this yourself by simply setting up your camera on a tripod and using a long exposure.
Sometimes Choppy is Good
I do prefer this look for water surfaces, but that is not to say the opposite effect is always bad. Just for variety, here is a shot in which I think the fast shutter speed, choppy water version works better: