So, how do you guys organize NPCs?
Well, I'm using Realm Works to organise my information for a book I'm writing. It's a historic novel based on real events and my list of characters has run well into the hundreds.
So what do I do?
First, we're talking kings and great feudal lords, so they all had this huge 'Houses' populated by officials, guards and servants (and respective families). So I use another software (because I'm very visual and the visualising of the relationships in Realm Works can't quite match the complexity I want), Labyrinth, where I can organise a diagram of who is connected to whom. Then I save it as an image and use that diagram as a smart map where I add pins to work as hyperlinks.
Then, of course, there are all the political and family links (important because of nepotism, where uncles and aunts often helped their nieces and nephews get good positions). I create more diagrams of how these people connect to each other, and have those images turned into smart images in a 'connections' topic.
That way I can easily go the the connections topics (based on House organisation, political intrigue and family networks) look at the picture-maps and decide which characters I'll want to use based on their personal connections.
So far, it's the best way of dealing with hundreds of characters.
P.S.: I'm avoiding containers because all the characters are very mobile: they move from one house to another, and a secondary character in one part of the book can easily rise to be a protagonist in another part.