I asked Any Finkel about this several years ago. I'll try to find his reply, but I may have nuked it. Anyway, he basically said the Tools directory on the 1.3 Extras disk was a mistake. It was meant to be Utilities, but once it was shipped that way, they just stuck with it.
The way I look at it, a Tool is something used to manipulate or create another project. Memacs, IconEdit, Editpad, etc. work with other projects.
Utilities are used to view other projects or display general info. Multiview, the clock, Amplifier, ect.
The System drawer I use for anything that directly controls a hardware device. Format, AsimCDFS, MasterISO, etc.
Of course, nothing really fits perfectly with the way the directories are laid out, but I'm most comfortable with this explanation. :-)