I think the PIM that would have - or might have - met Chris' requirement reasonably well isn't available any more. It was the old Claris Organiser for OS9 and earlier. Years ago now.
You had a calendar with appointments, notes, contacts, one or two other things. Then any one element of these could be linked to any others in some simple way. So you had a sort of ad hoc grouping of (say) a person's contact details, every appointment you had with them, every note of every phone conversation, and maybe the text of all correspondence. You got to each element of the set by clidking a link. And you could have as many of these bundles as you wanted. In addition there were the usual categories.
So Chris could have had journal entries associated with agenda items, or anything else. Snippets of code associated with a project. Reading lists from people at a given class. Anything at all could be made into a set and once you hit one, the others became available, but if you also wanted to look at items by category, you could do that too.
Later on it was sold to Palm and marketed in two forms, the Windows form of Palm organiser not having any of this linking functionality, but the Mac version kept on with it.
It was amazing. I kept looking for something like this too, and hoped maybe Chandler might turn into it, but alas... It may have been a functionality that was too obscure for most people to bother with, but once you got used to it, it was very powerful.
Al