Just about every stain can be easily removed ......... the exceptions are bottles that were buried for years in a wet area. Easy to clean are rust, cloudy areas or it's been sitting in an old barn for years. The easiest & least expensive methods (depending on how the stains were created) would be any product similar to Efferdent.  Walmart has their own brand I use at least 3 tablets per quart.  Leave about 1 inch of space at the top, as it will foam & overflow. Best is to leave it for about 24 hours even though the cleaning is done in a matter of minutes.   Stains inside of the bottle cans often be removed with "0000" Steel Wool.  Anything coarser will scratch the glass.  4 - 0 steel wool can be found at Walmart or a good Hardware Store.  Use a wood Moulding, or a hard wood dowell to rub away rust and stains.  NEVER USE A METAL ROD, SPOON, HANDLE, ETC. Walmart sells a product called CLR which stands for Calcium-Lime-Rust remover.  Just pour it in your bottle full strength & leave it for about 3 days for really tough stains.   A group of dirty bottles can be placed in a utility sink and soaked (inside & out) in a solution of a household cleaner like Lysol All Purpose Cleaner & liquid dish soap.  I soak them for up to 8 hours.  Drying with an absorbent cloth inside & out will prevent water spots. If you can send me some details of what the issues are, I can be of help. I do not charge for information, nor do I clean bottles.   If you want to build a tumbler, you can even remove water stains that are etched into the glass.

An Incredible Bottle Brush   I use a RubberMaid heavy duty (all plastic) bottle brush purchased at Ace Hardware.

Caution is advised for the following methods   The use of strong chemicals or acids may remove some stains, however, rubber gloves, safety glasses, a suitable work area and extreem caution is recommended.   Certain proceedures will etch the glass & ruin your bottles.