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It is not supposed to effect your CS 3 install. You do not have to deactivate if installing on the same machine.
I would however trash the preferences of everything connected with CS 4 before reinstalling.
As Wade said, deactivation is not necessary. What you backup is ultimately your decision, but if you have created custom workspaces, keyboard assignments, brushes etc. with the trial versions, you should salvage them. The uninstallers should not touch any of that, but better safe than sorry. Any such data is either in the Illustrator program directory (C:\Program Files\Adobe\Illustrator CS4) or in your user home directory (C:\Users\Diane\AppData\Roaming\Adobe\Illustrator CS4). The same applies to the otehr Adobe programs. In adition to using the CS4 Clean Utility, also make sure to uninstall Adobe AIR and Acrobat.com via your Add or Remove Programs panel. these are separate from the other uninstall, yet they can cause problems for re-installs.
Well, I uninstalled CS4 and unzipped the cleanup zip folder. (Not sure what they thought they were doing making the readme file a PDF when they just told me to uninstall the only program I have that reads a PDF.) The online instructions says to doubleclick CS4InstallerDatabaseUtility.exe and follow the instructions. After I say yes to the license it says I do not have windows installer cleanup utility installed and then quits. What is windows installer cleanup utility?