I'm my personal experience... Don't use Microsoft products that "help". They really don't, and if they do, their minimal. If you're looking to clear/clean up your drive, then I suggest using CCleaner, IOBit's Advanced System Care Free (warning Advanced System care by default turns off the option to record any Blue Screen errors, you have to stop it from doing so), and also deleting any files that you don't need to have. If you're using the C: drive as a dedicated OS drive and have a second drive to store other files, make sure that your documents drive point to the second drive.
If you are using the hibernation options within Windows, then deleting the hiberfil.sys associated with that will also help. This is where the "Windows Cleanup" should be useful, however a manual deletion and disabling may be necessary.
I would also suggest using a Defragger like Piriform's Defraggler as well, as that may help things out as well. (Note: Windows 7 automatically takes care of defragmentation, but I feel that it doesn't do a good enough job)
Finally, 40 Gigs just doesn't cut it any more. Even for a dedicated Windows OS, that's cutting it close. Once Service packs, and more updates come along it will be cutting things really close. I would suggest looking into purchasing a larger drive. It'll save you in the long run.