The problem with the store warranty is that oftentimes, they're not equipped to handle problems for your specific brand notebook. For example, Best Buy's Geek Squad is not a Toshiba authorized repair facility. If you have a Toshiba computer, and you have them repair it, it will automatically void your computer?s standard warranty because you let an unauthorized repair facility fix your computer. By going with the manufacturer's warranty, you are being assured that the manufacturer stands by your product and will repair it to original specifications.
Personally, I have bought both a store warranty (with an emachine's desktop) and the manufacturer's warranty with both of my Toshiba laptops. The emachine was a lemon and the store refused to repair the device to my satisfaction, citing reasons including, "it?s not worth our time", "we're not authorized to do that repair", and "that'll take 6-8 weeks to complete."
On the other hand, with my Toshiba laptops (with manufacturer's warranty), my lemon laptop (I seem to have huge problems with a lot of my computers) was repaired in under 36 hours and delivered to my door. After multiple repairs for the same issue, Toshiba stood by their product and replaced it with the same model.
The difference is that you have the manufacturer's backing (who has an interest in making sure you're satisfied with their product) versus the store's backing (who has an interest in keeping you and your problem computer out of the store and taking your money to pad that quarter?s balance sheet).
I wish extended warranties were not a fact of life and manufacturers would include 1, 2, or 3 years of service support with the computers. I would also love to see everyone join Consumer Report's call to boycott extended warranties. But I?ve had enough problems with computers to understand that 1) you need an extended warranty and 2) you should get one from the manufacturer.
Don't let store personnel tell you otherwise! They make a commission out of these warranties. I?ve had both a Best Buy and a Staples representative tell me that the manufacturer does not sell extended warranties and that if I break the machine once I leave the store, they will not do anything for me. This is a huge scare tactic. Don?t be fooled!
I hope all of this helps!