I am in the process of redoing my displays, so I've been thinking on these issues a lot lately. Here are my long-winded thoughts!
I used to use cheapy freestanding cubes (the kind they sell for college dorm storage) because I had them hanging around. The problem with these and most other types of shelving is that they're around 12" deep, while most game boxes are less than 6" wide. You get that annoying thing where you try to keep all the games near the edge of the shelf but then it's impossible to actually remove a game without messing up the whole system. Plus, having a too-deep shelf is a waste of space in the room.
I finally decided to redo my displays with elfa shelves from The Container Store. I used to think CS just made wire racks for the kitchen or garage, but they have melamine shelves that look more like wood, too. They make an 8"-deep shelf that is much more compact and great for games. There is still a "dead space" problem, but it's much improved from the 12" shelves. You can adjust the heights on these shelves to match the height of your games, too. (Aside from being too deep, most shelving is also too tall for video games, resulting in more wasted space.) They have snap-on bookends, sliding baskets, etc. if you want to get fancy. BUT tl;dr: Short and adjustable shelves mean less wasted space, more games per square foot.
I have my games split up so that all the loose carts are in one set of shelves while all the in-box games are in another set of shelves. Within these categories, they're then organized by console date order. The result looks tidy because the NES, SMS, Genesis, and SNES boxes all pair together and are about the same height. I put the NES carts up on their sides, while SNES and Genesis carts get stacked up because those don't like to go on their sides. I don't have many N64 carts, so I don't have to worry too much about the end label issue.
Whenever there's a weird spot in the collection (transition from boxes to jewel cases, ugly bracket that needs to be covered, etc.), I reach for something from my game goodies pile such as a Nintendo plush or figurine to act as a bookend or decor item. Let those items serve a good purpose while being on display!
OK, I have more to say, but I think I'll stop there for now.
Hope this helps!