[@Nerdy Reference]
Organizations for the most part can be used as they can be easy to incorporate into a single world.  That said certain organizations might be too big and influential to mesh well so it is kind of a case by case basis.  The BPRD in the spawn sheet is something that is very easy to incorporate and make sense in a modern day world type setting.  The Black Order I feel is why too dependent on the universe it comes from to really fit well in this world.

Likewise something like the brotherhood of Nod is way too big of an organization and too specific to the franchise it comes from to fit anywhere in this setting.  People couldn't really be living normal, ordinary lives with something like that on the scene.  While I really don't think Shadowrunners could fit in either, due to game lore, but I will say there can be cases of specific cities or nations that could be rather 'special' due to certain circumstances/lore.  In general if you want to try for an adaptation you'll have to severely limit the scope of many elements for it to work.

[@Indra]
Hmm...Naruto would be a hard one to squeeze into a modern day setting.  I suppose if you separate characters from most of the lore it would be possible...I'd have to see the results to say for certain but I'd probably be a pretty harsh judge on something like that.  Sounds like you at least have an idea of how to do that so, curious what you got if nothing else.