Actually according to Apple, it shouldn't matter if you leave the iPod on the charger all day long, and you don't need to run it all the way down before charging it again.
http://docs.info.apple.com/article.html?artnum=62018#7 That said, I do not know if they would make the same statement regarding a third-party dock/charging station like Bose.
What definitely does shred the battery is letting the unit get very warm while charging, like charging it when it's inside a leather case.
You can do-it-yourself replace the battery-- lots of sites online for how-to's. It is a pain the first time around, till you see how it all comes apart and goes back together. After that first time, it is actually quite simple. Just remember there are a lot of delicate cables and connectors inside, and be gentle. Apple will swap the battery out for you-- actually they just swap your iPod for a refurbed one of the same model, and given the price they charge, I don't think it's worth it, especially since you have to reload all your music and it takes longer if you want any engraving put back on it (mine says Reward if Found on the back and has my phone number and has helped my iPod find its way home when left on a plane). Lots of services online will do this faster and cheaper than what Apple charges.