I have determined that my 2002 Eclipse Spyder leaks water into my car when it rains. It appears that most of the water is on the driver side (front and back). Does anyone know of some common places that the eclipse leaks and how you would fix it?

look for major tears in your weather stripping-If its bad replace it,
Or just looks like crap use baby oil will replenish the ugly cracking. or so auto body classes tell me.

I dont think anything is worn, but its more like a factory defect/bad design. Go to the dealer and they have special seal kits that they install to stop leaks

NOOOOO dealer overpriced.
Just get a Dark rubber friendly sealant.

you can always use a black rubber sealant from home depot and once it is dried, but not yet cured.

you roll your window up, not all the way but enough so it pushes on the sealant this will form the sealant to your window's contour. (in know its hard to do with automatic windows, but it is possible.)

then roll it down and let the rubber sealant cure.

this will completely seal your windows, not only from rain, but also from air when you roll it up.

dry ride and quieter as well.