Don't use caustic soda as it can indeed harm the glass. Teddio's suggestion of warm vinegar is good but if you'd prefer not to have vinegar fumes around, a good alternative is a fairly strong solution of citric acid, obtainable from chemists and home-brew shops as well as ebay etc.
Buiders tend to use dilute hydrochloric acid contained in certain brick and patio cleaners to remove lime deposits but it's nasty stuff and you really need to wear protective clothing and eyewear during use as well as following the instructions closely.
Another alternative is a substance called EDTA or it's salts which are used extensively in laboratories for the removal of calcium deposits. EDTA is less hazardous than hydrochloric acid but you still need to adopt a common-sense safety approach. The solubility in water varies between the salts.
Finally, commercially phosphoric acid is another acid that's commonly used to remove limescale. You've probably got some dilute acid at home right now in the form of Coca-Cola or Pepsi etc. Leave a 2 litre bottle of the stuff go flat by removing the bottle top, pour it into a bucket and immerse the bottles from hours to days if need be. Top the Coca-Cola up as necessary. I think you'll be surprised by the results and it won't harm the glass.