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My Laptop is getting slower and slower. I is almost 5 years old now. I am dual booting Windows 7 and Ubuntu 12.04. On the Windows side, I have two partitions and both have plenty space. I did a full scan with Avast and Malwarebyte and no virus is found. I tried to clean out the temp and other trash, disable aero and almost other stuff that I can do besides disabling my wallpaper (which I know doesn't make a big difference in performances) What happen to my computer? Is it the CPU normally slows down over time? Or other things?
Over time computers just slow down. It is a lot of little things that just add up. You can run CCleaner which will help delete some useless stuff. Defragmenting your hard drive will also help.

What I would recommend is a re-installation. Then once you have your system set up perfectly make an image back up of your OS. That was once your computer starts to slow down you can just restore from this image and it is pretty much as good as new. I do this every couple months.
I have ccleaner installed and I use it almost everytime...and I defrag almost every week.

If I want to reinstall, but I am dual booting with Ubuntu 12.04. What is the proper way to reinstall?
Well with my laptop, i normally will do a full factory reset every year, b ut if you dont want to do that, one thing you really should do. is use a compressor and blow all the dust out of it, that will help it speed up a bit.

and if you run a defragmentor tool, it will really help you out.

there is many other things you can also do, pm me if you would like to know more.
Factory reset, only suggestion i can give.
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It has 3GB of ram, max out. temp is around 60c ~ 80c. Windows 7 ultimate sp1, 1 year old.
I'd suggest doing a Factory Restore.
My personal preferences when that occurs is to reformat the thing. Always makes me happy and gives me a sense of accomplishment when I see my machine working as if it was new again.
Quit dual booting it and freshly install windows 7