After 20-odd years I've just started using the "Expansions" directory. I use this for hardware-related utilities (eg CyberSCSI, ie utilities for hardware "expansions") as opposed to software utilities (eg Snoopdos).
Every time I re-install the OS things end up in different places though. Comes from having a small OS partition, and then dumping program installations into a large "work" partition. Don't know exactly why I ended up doing this, just a habit I've picked up over the years I suppose. One day I'll get it all exactly how I want it....