The tools archive contains two plugins, the DeDRM plugin which handles ADE/Amazon/B&N, and oboK, which handles Kobo Desktop.
You can of course use the Windows application which only works for Windows and runs independent of calibre, if that floats your boat...
(This is all explained across a couple blog posts and the readmes, too.)
Either way, I do advise you to DeDRM your books -- the way I see it, you chose Aldiko specifically because it works with DRM. There are a number of ereader apps out there, and you might very well decide you enjoy reading in another app better than Aldiko, but you can't even try until your ebooks are set free.
