I realized that charging my HTC Desire (Android 2.1) takes longer if connected to computer compare to power outlet.
Does it matter which method I use to charge in terms of battery life time?
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No, the battery doesn't care how it got charged in terms of a given charge. It just takes longer when using your PC because it's getting less current from the PC than the AC charger.
Here's a post on android forums which suggests that the current coming from the PC is significantly less than the AC charger. The forum posts list 100mA or 500mA for the PC's USB port vs. 1000mA from the AC charger; these numbers could be off but the point is correct. I also found this regarding the same phenomenon with the iPhone 4.
So using the AC charger is just a matter of whether you want the phone to charge quicker or not.