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Ebooks: I use Calibre locally and Calibre-web on the server (read-only metadata db, I overwrite with the Calibre version as tagging, etc is far easier on desktop).
You can connect Koreader to Calibre-web and until maybe a fortnight ago you could jailbreak a Kindle and use Koreader instead of the default software. Now you'll need to manually move files over, or use the email-to-Kindle option (probably a bad idea, but I expect Amazon can tell if you've side loaded pirated content anyway). Nowadays I buy from not-Amazon sources, strip any DRM and send it over.
Manga/comics/graphic novels: I use Kavita on the server and I use comictagger on desktop to fix the metadata.
I'm happy to use different set ups for the different types as they're quite different experiences and specialist tools work better.
Where do you get DRM free ebooks for sale?
Ebooks.com has a ton of DRM-free ebooks. They have a whole DRM-free section, plus a search filter, and they clearly display all available formats before purchase. That's my first stop for ebooks.
None of the books I've bought from kobo.com have DRM.
Just to be clear, I'm pretty sure that they don't have a no-DRM-across-the-board policy, though, so if you're going there for DRM-free ebooks, you probably want to pay attention to what you're buying.
checks
Yeah, they have a specific category for DRM-free ebooks:
https://www.kobo.com/us/en/p/drm-free
I'll also add that independent of their store, I rather like their hardware e-readers, have used them in the past, and if I wasn't trying to put a cap on how many electronic devices I haul around and wanted a dedicated e-reader, the Kobo devices would probably be pretty high on my list. When I used them, I just loaded my own content onto them with Calibre, not stuff from the Kobo store.
I guess I've just been lucky then! I've stripped DRM off everything else, so I expect theirs would come off using the same tools.
If you are in germany, thalia lists whether a book has DRM