I agree there is nothing quite like Tinderbox and I use it extensively and appreciate its many affordances. In particular:
- Outline structure
- Note attributes
- Map view (spatial hypertext)
- Links and link types
Whilst I work on specific projects in Tinderbox my ‘knowledge base’ application is actually TheBrain. This allows extensively linked notes. In version 12 it will offer more Obsidian-like features but you own the data and the company has a long pedigree. My other reason for using its is that it is cross-platform Mac/Windows/Web/iOS/Android.
Like lots of Mac users my ‘bit bucket’ application is DevonThink Pro. Mac only though.
Tinderbox and a few other key applications are a great reason for using a Mac. Many more small software companies producing great software in this ecosystem but that may be just a matter of opinion.