Currently this list is pretty unorganized. I am adding things as I organize my browser shortcuts and I find things that are worth passing on to anyone who visits here. All of these links will open in a new window.
Sky and Telescope's Jupiter's moons JavaScript utility -- This "applet" allows you to see the position of Jupiter's moons for any given time and adjust time forward and backwards in 10 min, 1 hour, and 1 day increments. I use it to look for transitions and shadows that might occur when I am observing.
Selenographia - the Inconstant Moon Atlas -- This site provides a nice atlas of the moon that you can view in high resolution with some basic navigation tools.
SEDS Messier Database -- Check out the icon sheet and thumbnail index methods for accessing extensive information about all the Messier objects. Provides nice photos of all objects as well.
Stellarium - Free planetarium software -- Free and it's just plain cool looking. I have even used it to substitute for traditional charts.
Pablo Lonnie Pacheco Railey's Awesome Lunar Picture -- A very nice composite image of the moon, suitable for creating a lunar atlas!