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with windows xp that you could set entire folders to be stored as compressed, then windows would compress / decompress indiividual files as needed. so you'd have your entire library in compressed folder, under the hood, yet calibre would work as normal & you'd have no need to mess with individual files formats.
in win 7 you right click calibre library goto properties ...advanced ...tick compress file to save space... then select apply to subfolders. I suspect it will not save much space tyhough, unless you have a lot of. txt, .rtf format books.
the epub, mobi, zip, pdf formats are already compressed, so compressing them again is not going to help much.
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