When people speak of storing water and having it 'go bad', all we're talking about is bacterial growth, right? I am assuming that if the water was good to drink when it was put into storage, other contaminants were eliminated before storage.
It seems that if you are using municipal water, you should be able to ask for a copy of the test results. I belong to a local water association which mails out the test results twice a year. This is a pretty complete test, not just bacteria.
If you are using well water, it would probably be a good idea to get a full test done occasionally. It isn't cheap, but it would be good to know. It might also be useful to find out what kind of water source you're tapped into. I guess sometimes it's a true aquifer, and sometimes it's just groundwater. Contamination with manure nitrates and farm and industrial chemicals are more likely with some than others. And don't forget all the lawn and yard chemicals that are transported into your water supply. Not to mention dumped petroleum products, flushed medications, and a host of other contaminants.
It would be interesting to store your water for ten years or so, and open a bottle every year and have it tested for bacteria (it's usually about $10 around here). Of course, if you ran into problems early on, you would know not to try to store it past that point.
Exposure to elevated temperatures might also affect bacterial counts.