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I've read the best thing for your battery is to run it completely out. But when my battery is nearly empty my vaio goes to hibernate. I've set a message for 10% to give an alert but no actions. Is this normally or can you change it?
You can change what messages you get and what the computer does at 10% and 5% in Control Panel>Power Options.
I don't think I would run your battery completely flat - I'd set it to go into Standby at 5%.
Have you tried the free trial version of BATTERYMATE XP
This link will tell you everything you need to know about batts
http://www.batteryuniversity.com/index.htm