1) Why remove as many applications in Safe Mode?
You dont have to remove all of them, just the ones that you know you are not going to use. The reason why you do it in Safe Mode, is so that the computer will have a better chance of cleaning it properly. While you are already in Safe Mode, it is a good idea to go ahead and empty the trash and then defrag. If you have any questions on the specific applications that you have listed in the add/remove programs, feel free to post them here. I will go over them.
2) After defragmentation, I need to turn off the computer by physically turning it off or by perfroming a shut-down?
That is a great question
! After you have finished defrag, you want to shut down the computer like you normally do. Some computers are different then others, but in almost all cases, you will use the START -> turn off computer. Models vary on if it displays "it is now safe to turn of your computer."
The reason why you want to wait at least 30 seconds before you bring it back up, is because that is what you are normally suppose to do. Have you ever noticed that when you are close to a TV and you turn it off, you hear small popping sounds. It is from the static electricity in the air, close to the electrical components. If you turn the TV back on right away, you stand the chance of that static charge arcing back to the TV. The same is true for the computer. Granted-it is a VERY SLIM chance, but why take the risk?
We are all curious like a cat. We wonder, we ask, we learn.
Please post back when a suggestion works, so that others may learn.