Thought I'd show some examples.
Here's a wooden organizer thing:
It's designed poorly because there's no way to fill it up and set it on an appropriately-sized shelf and access the games. Pulling the drawer out far enough to access the rear row essentially just pulls the whole thing out and it's a pain to put back in while fully loaded. If you don't use an empty flat space with double its footprint (equal space in front) then the games will unbalance it and send the whole thing to the ground. Trying to suspend it and get a game from the back row guarantees that the drawer will come completely out and you are going to be putting it back together on the couch.
Even so, I kinda like it. It fits a lot of games and came with some kid's "Best" and "Very best" Metroid passwords stuffed into the top.
This shelf has a row of boxed games in the back and many more in the aforementioned "appropriately sized container" (front). Also visible here are some of the "just loose" games. So sue me. There are even more loosely piled at our other place (some cased, some sleeved, some loose; no pics). Sometimes I find perfectly sized containers that just aren't strong enough, so I patch them up and use them anyway.
Here's another huge shelf of games in cases:
I actually have more cases than will fit on the shelf but not nearly enough to start a second shelf (most are at the other apartment where we also have many sleeve-only games (no pics).
More "appropriately sized containers:"
You can see that I turned one of those boxes inside-out when I realized what it was good for.
I usually leave these in front of the cases games because it's a deep shelf and I can slide these left and right to access the cases games behind.
Here is another "purpose built" organizer I put in front of the cases games:
It's nice to have a place to put some of my loose manuals that don't have a box.
These aren't for NES, but here are some containers I've adapted or strengthened for SNES/SFC games:
All in all, it's cobbled together and not very presentable, but it's better than leaving it in piles... which reminds me that I still need to take care of that pile at my other place (not pictured).