Why not have both? For my technical journals I keep while working I use org-mode in Emacs. You can slice-and-dice your entries in many different ways using that package.
However when I'm reading specifically I keep notes in paper journals. First I find the immediacy of pen to paper to be intuitive. Second, and more importantly, the serial nature of the journal forces me to explain my thoughts. It is this specific constraint that allows me to see the process I went through to arrive at my current self.
It's not indexable or searchable, that's true. However I don't need the process of reflection to be fast and instantaneous. I have a lifetime to work it out. I don't mind reflection and introspection to be slow and tedious.
Perhaps it's not the most 'private' solution, but you might enjoy keeping a diary at www.dabble.me , you get an email everyday with an earlier entry (like from 1yr ago). It's a great source of relativation to track your old emotions and to rediscover old insights. I think you can run it on your own private server if you want to.
However when I'm reading specifically I keep notes in paper journals. First I find the immediacy of pen to paper to be intuitive. Second, and more importantly, the serial nature of the journal forces me to explain my thoughts. It is this specific constraint that allows me to see the process I went through to arrive at my current self.
It's not indexable or searchable, that's true. However I don't need the process of reflection to be fast and instantaneous. I have a lifetime to work it out. I don't mind reflection and introspection to be slow and tedious.