I only have a small selection so I just keep them in the packet that the Sanrio cards came in, and they're currently sitting on my shelf next to my games.
I've got my cards in the Series 1 binder (cause thats all I have). My Sanrio and amiibo Festival cards are in the back in the spare sleeves and the duplicates are in a pile.
I have them all precariously balanced on top of my NFC reader which is sitting on my bedside cabinet. That way I can grab both of them at the same time if I'm wanting to scan anything in, if the cards don't topple over that is!
I keep my 18 WA cards in a pile, tied with a rubber band so they stay in their stack. I keep my 12 regular Amiibo cards in one of the packs I got them in.
Example of WA Cards: