IIRC they were used in the 707/727 days for taking star sights. Since the 737 shares the same fuselage, the eyebrow windows got carried forward. I remember reading an article from Boeing which said they were deleted to reduce the cockpit noise levels. Aircraft without the eyebrow windows are also equipped with 10 vortex generators just forward of the main windows. Boeing claimed a ~3 dB (not sure of the value) reduction in noise and appx 10000 $ per year reduction in mx costs. They offer kits for the older acft to remove the windows and install a plug in their places.
Please feel free to correct me
Cheers
PS : I believe they deleted the window in the NGs from mid 2005 onwards.