Ok, so I asked the same question about water stains in the Q&A...
Mine are TERRIBLE! I am a perfectionist though... anyway, whomever said 2hrs, I have spent in excess of 8hrs on my glass! Car came from Victoria.
The reason the glass does this is people not washing dirt off, it rains, dirt pools, sun bakes it in. Repeat for X years, and you end up with shitty looking windows! Hard water will also have this affect.
Polished with microfibre (it was a not cut polish) and it gave an overall clean, but didn't go close to removing marks.
Tried the vinegar, did nothing.
Hamish said 0000 steel wool, I was sceptical. I did it, and it did make some difference. I did scratch a window in one spot (probably was a bit zelaous), but the rest were fine. I used a reasonable amount of pressure, a smidge bit of water from a spray bottle, and made sure the window was CLEAN AS! I used 3 cloths to post clean to remove any steel wool bits left over, and I taped up my plastics so as not to scratch them, or have steel wool bits fall between.
I am still not happy. Hamish suggested if not 0000 wool, cerium oxide. Given the time I have spent on the windows already, I have lived with it for 8 months, but when uni is over, I am buying some cerium oxide and giving it a crack.
Maybe the hydrochloric acid is worth a shot as well...
Moral of the story, regularly wash your windows if your car sits in sun all day.