"00" (double zero) steel wool works great. Soaked in vinegar makes it even more effective. It won't scratch glass. But be careful with the trim and paint around the windows. Even 00 will take the finish off plastic and rubber trim and isn't very nice to paint.
I use this window cleaner that the glass company whom replaced my window gave me. I'll post up pics of it so you can possibly get something like it. It works great. You just spray it on and wipe it off with a paper towel. No water spots, no streaks.
I've always used super fine #0000 steel wool on tough spots. If the spots are stubborn then I'll pull out my buffer and compound and polish the glass. Usually the steel wool, plain water and towels get it done for me.
