I use a 16 oz. plastic "stadium" cup as my measure, and record it in FitDay when I finish one. (I keep a FitDay window open pretty much all the time when I'm at home.)

I have always had trouble keeping up with my water intake, so I have to keep coming up with ways to increase my water. The latest trick I've devised is actually kind of recursive: since more water = more trips to the bathroom, whenever I'm done in there I fill a 4 oz. cup and drink it down before leaving the room. Seems to be helping; I've increased my intake almost 150% since starting that.