This may not be new to some, many of you may do this already, but for those who may not have thought about it I figured I'd pass along this hint. As I'm a birder, I love to garden for hummingbirds & keep a lot of hummingbird feeders. Those of you who use hummer feeders also know that you can buy little brushes, some made of bristle, some of soft sponge, to clean out the hummer feeders. Hummer feeders are very similar in size / shape to hamster bottles and the brushes used to clean them are excellent for getting inside the hamster bottles to give them a really good clean!
Many bird stores sell these small brushes (I personaly prefer the small sponge tipped brush) for just a couple of dollars. You can also get the tiny "Mascara" shaped brushes which are used on hummer feeders to clean out the ports. These can also be great for cleaing inside the spout end of the bottle.
(For those in the UK, as you don't have hummers there you probably won't find the hummer brushes but I'm sure brushes of some sort do exist for pet bottles)