My game shelves are a source of constant reorganization. The current system: large boxes spine out on dedicated shelves, small boxes and card games in a dedicated small-box section, expansions in the same shelf section as their base game, insert-upgraded games in their original boxes. Everything is alphabetical within sections.
The real question is whether to keep box art visible. I prefer spine-out for space efficiency but there is something satisfying about a shelf that shows the box art. A rolling display system using card holders can show art while keeping boxes spine-out — I have seen this done beautifully at local stores.
Storage for games without good inserts is the harder problem. Broken Token and Folded Space make inserts for most popular games. The cost is real but the gameplay improvement from a well-organized insert is also real — setup time drops dramatically when components are well-sorted.