I have lost countless notebooks and other notes on paper. For those I haven't lost, I find it really hard to find what I'm looking for. I started consolidating my note-taking in google docs and haven't looked back.
Seems like you might need a better indexing system -- table of contents in the start of notebooks, and perhaps a directory consisting of copies of those ToCs in a loose-leaf binder for the entire set?
How valuable is your past journaling with such a system?
I use a mixture of Vim with text files, and the Windows Sticky Notes app, for my notes. The text files go into a folder related to what I'm taking notes on, and are for longer storage. There's usually other file types in there too, and the folder can be backed up and/or version controlled.
Short-term and quick-access notes are in Sticky Notes, which plaster the desktop on one of my monitors. That's where I keep meeting notes, TODO lists for the next day or two, time-tracking if I'm not putting it directly into my time-tracking app, etc. Generally, none of that is worth saving beyond its immediate usage.
I've rarely needed to refer back to any of this stuff beyond the few days where I'm using it (Sticky Notes) or the duration of a project (text files). I don't delete the text files, but I hardly ever need to refer back to them.
Various other methods are also in use. I've found journals less than intuitive, as there's a distinction between keeping a notebook vs organising/recording routine activities and events that I find difficult to span and/or separate.
Online/electronic systems remain insufficiently flexible for daily activities, though I've gone through several iterations of shell / vim / org-mode systems.