It will depend on the plugin and how it is installed/authorised.
If you uninstall AE CS4 any third party software files should remain untouched in the folders:
Adobe/Adobe After Effects CS4/Support Files/Plug-ins
or
Adobe\Adobe After Effects CS4\Support Files\(Media Core plug-ins)\Common
You might want to make a copy of the plugin contents of these locations before the AE re-instal (What I like to call a drop folder). Although you wont be able to back up any registry keys that many plugins use for authorization (unless you know how to find them!) you should be able to first of all see what works and what doesn’t in the fresh AE then (making another backup of the same two folder locations first) over write from the drop box to see if that gets any more plugins working. I wouldn’t have too high expectations but it might save you a little time at least!
I find drop folders a great time saver and use them for plugins in many apps and even for my own scripts, support files and UI settings.
Graham Macfarlane
3D animator and VFX specialist
London UK