A lot of people use third party cleaners, rather than Windows disk cleanup. Personally I like BeClean, which is easy to use and will run on Win98se:
Unless you are very short of space I would not delete duplicate files, it is too easy to make a mistake.
Have you run Windows defragmenter lately, that can help.
And finally check what is running at startup, can you disable some items to give your system a boost. StartupRun is handy little tool, to show start up items: