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Technically nothing needs to be on the SD card. Certain apps store data on the SD card it would be *nice* if they all shoved their data inside of data/ directory but they don't. A lot of apps don't remove their directories after you remove the app either.
Best advice I have for you is to dig through it. Delete the directories that belong to apps you no longer use. You can also organize photos, music, videos and documents however you like.