When applying the patch this error can happen:

    checking file skin/adminhtml/default/default/media/flex.swf
    checking file skin/adminhtml/default/default/media/uploader.swf
    checking file skin/adminhtml/default/default/media/uploaderSingle.swf
    Reversed (or previously applied) patch detected!  Assume -R? [n]
    Apply anyway? [n]
    Skipping patch.
    1 out of 1 hunk ignored
    checking file skin/adminhtml/default/default/xmlconnect/boxes.css

The 8788 patch contains binary content. As Magento does not provide any direct download links (I hate this policy ever since), you have to download the patch to your computer and upload it with an file-transfer application (like WinSCP on Windows) to your server. WinSCP for example will upload in TEXT-mode (WinSCP handles *.sh files as text by default).

So the workaround for this is, zip/tar the patch-file and unzip/untar again on the server. et voila.