If the stains are on the inside it's probably algae if the bottles were not washed out straight after use. Fill about quarter full with sand, add to half way with water and give a "cocktail" shake. Rinse with clean water. Make a mental note not to leave them again!
aluminium oxide is very tough stuff, you might get it off with caustic soda (which is a bit nasty to use) but other than that you would have to sand you bottles back which might make them look a bit messy
perhaps your best option is to buy some darker bottles
yeah well no bike shop is going to hand over a pair of really good cages for nothing....
there is nto much you can do except get some different cages or darker bottles. You can't get rid of aluminium oxide from the cages since it forms instantly when polished aluminium is exposed to air and forms a hard protective layer on the surface that stops them corroding further
Darker bottles is not really the answer. They stain as well. I use sunlight liquid and those green pot sponges and that cleans them quite nicely. I have bottles that I use for more than two years now and just clean them after every use.
Been a while... When washing bottles be sure to sterilize the bottlles AS WELL AS THE MOUTHPIECES very carefully. You do not want somebody elses stomach on ARGUS morning!!!!!! Use Milton or normal UNSCENTED bleach (you do not want your water to smell like a spring garden or apple blossom!!!!) Leave the bottles upside down to dry, close the mouthpieces and put the caps back on. Be sure to rinse the bottles carefully to get rid of the Milton/Bleach. Anybody with babies out there this should almost be routine!!!!! The sand idea to get rid of Algea spots will work. Just remember sand can carry a lot of bacteria (flea eggs, faeces etc) Sterilize the bottles very very meticulously after scouring with sand. On the black spots....learn to live with it....millions of other cyclists do. Also dump your bottles regularly and get new ones. They are cheap enough. You can use the old ones to pre-race hydrate when you stand in the starting blocks. Be sure to dump the bottle in a garbage can.