I think you can create a directory for all manually installed plugins: media decoders, compressors, Avisynth, any DLLs required by applications. Then add this directory to your PATH environment variable (Win98 -> Autoexec.bat, WinXP -> Control Panel / System / Advanced). This way you'll keep all plugins if you decide to reinstall Win and can easily find and manually update them if they become obsolete.
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