I am afraid writing my thoughts and reading them will cause them to lose their affective components.
If I have a really good idea, I might write myself a note, but I won't try to describe the whole idea -- if I do, it's like my mental model loses any complexity that couldn't be expressed in my description. Perhaps a paper mindmap might prevent this from happening.
Perhaps you could create an index of affective or untranslatable responses along with stimuli that produce them. You could then reference this index in your notes.
Related to: Living Luminously
Well? Should you?
Linked is a treatise on exactly this concept. If the effects of recording and classifying every thought pan out like the author says they'll pan out... well, read a (limited) excerpt (from the Introduction), and I'll let you decide whether it's worth your time.
The full text is written in a stream-of-consciousness style, which is why I hesitated to post this topic in the first place. But there are probably note-taking junkies, or luminosity junkies, or otherwise interested folk amongst LW. So why not?
(Incidentally I'm reminded of Buckminster Fuller's Dymaxion Chronofile. I wonder how he managed it, or what benefits/costs it wrought?)