Sync Apps from iTunes
The best way to purchase and maintain your apps is to buy them through iTunes and then sync them to your iPad while it is connected to your computer. While this does take a little more work on the user's part, it helps to guarantee that no problems occur during the transfer to the iPad, or to your iPod Touch or iPhone. The same principle applies regardless of which device you use.
By first downloading into iTunes, you are archiving the app onto your computer's hard drive. It is placed in your iTunes library where you can delete it or choose whether or not you wish to transfer. Through iTunes, you will also learn if there are any updates for your apps. By first putting the app in your library and storing it on your computer, this guarantees that you will still have the app in the event that something happens to your iPad such as physical damage or some problem that prevents syncing.
With any electronic device that deals with software and files, there is a possibility of data corruption or faulty programming that can cause the device to malfunction. I've personally had to reset my iPod after it had gone without a charge for too long. I've also had to wipe and resync my iPod Touch after some software updates caused it to stop communicating. Luckily, I had my entire iTunes library backed up so it was no problem to restore everything just as it was. If I didn't have that iTunes backup, I may have lost all my music, apps, and movies.
Image credit: iTunes screenshot @ Author's PC (Serial number removed for security)