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Bleachbit is safe enough as long as you choose the correct items to be cleaned. It is *not* useful for getting rid of bugs, your intended usage - if you have bugs in a system then you need to address these otherwise.
Although Bleachbit has only, in my experience, affected the operating system on which it is running, I would advise that to ensure that Bleachbit doesn't affect any other filesystems on the hard disk, unmount these filesystems.
Personally, I run Bleachbit both as user and as root with the following items checked to be cleaned (this is specific to me, your mileage may vary):
(user) Bash, Chromium (exc. Form History (generates error) & Search Engines), Firefox, Flash, GIMP, GNOME, Google Chrome (exc. Search Engines), Java, LibreOffice, Opera, Skype, System (Cache, Clipboard, Recent documents list, Rotated logs, Rubbish Bin, Temporary files), Thumbnails, Thunderbird, VLC, WINE, winetricks, X11.
(root) as above + APT.
If you're running Bleachbit for the first time, it is highly recommended that you make a system image first so that you can easily rollback if something goes awry.
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