The closest I've found is Workflowy, but it's just that bit too basic.
I store all web clippings in Evernote and hope to find what I want one day.
I bookmark heavily into an online service, and wish my tag vocabulary was better constrained (but full text search helps).
And finally I mind map on paper; none of the digital ones have quite cut it.
One day there will be a PIM to rule them all. One day.