Give me a peg board wide and  long enough and enough pins on which to place it, and I shall know of every tool.
Tools should be organized for convenience, what one person finds convenient another may not. The only things one really must consider is, ease of access and suitability to location.
If water can damage a tool in a night it should not be stored in a humid room.
If a tool can leak a fluid of some kind it should sit in a basin. Tools in a bucket is a fast way to damage