I use a White Vinegar and water mixed 50%. I always keep a spray bottle of it near at the work bench. I use it on the rear fender as well before I put the passenger pillon on to get any dirt off the finder before the suction cups go down.
I use S100 total cycle finish restorer. It seems to work pretty good for the strips of aluminum on my Fat Boy Lo wheels. I recently got a lift and it makes it a lot easier since you can just turn the wheels to get to unpolished areas instead of getting on and off the bike and moving it around. I have also started using an Air Shammy dryer which has helped reduce the water spots. It cost quite a bit less then the Air Blaster dryers do.
White vinegar will disolve the calcium in the water spots and get rid of them. I live in nevada and deal with hard water all the time, I usually dry the bike off pretty quick and dont get the spots, but if i do, the vinegar works great.
Try the towel trick given by kyleplusitunes...I had the same prob last year and just put forth the effort to dry it more efficiently (properly? lol). Chrom polish will also take the spots off no problem....a lil elbow grease!