I have noticed that when I use the Synaptic's option "Complete Removal", the hidden configuration files/folders in my home directory are not removed. Some people told me that is because when I reinstall the software I can re-use my previous configuration... I totally disagree with that way of thinking, because if it is a complete removal, it should be complete (i.e. remove all files, including configuration files), for the other situation there is the (plain) removal option. Ubuntu as you know release a new version every 6 months, after 6 months of using a release, meaning not only using the software but also trying (installing, removing and updating) different software packages, my hole directory is a mess. The only way I know to restore the directory to the "original clean initial state" (that is not so clean and ordered) is to do a fresh install.
A second reason for doing a fresh install is to 'test' if all my hardware is correctly detected and configured without any intervention (For example, in early versions I do remember having to modify my profile (.bashrc) in order to have my wireless card working).
Because of these two reasons I do a "fresh" install.
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You could get the same effect by creating another user account, avoiding the whole re-installation procedure. Alternatively you could just delete the dot files/folders for any applications you no longer use.
The reason for Synaptic not removing those files/folders is a) the packages don't know about them - they can only remove what they installed - and b) those files/folders can contain information that shouldn't be removed automatically.
On my old machine I happily upgraded through a couple of releases, and on my current machine I've gone from Feisty through Gutsy to Hardy with no problems. I've only recently performed a new installation of Hardy so I can switch to 64-bit, and for the majority of applications I'm copying the dot files from my old home directory verbatim - a simple copy and my Firefox had all my old extensions, bookmarks and stored passwords. When it's time for Intrepid I'll be upgrading again.
Whilst there is something to be said for a fresh install - after all how can the installer be tested if no-one uses it! - the practice is less useful than it used to be.
As for testing your hardware, just use a LiveCD or the Hardware Testing application under System > Administration.
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