I used to use the number two pencil for this kind of thing, but I find
that while it works well with looseleaf paper, and (my preferred tool
for "analog storage medium") the unruled three-buh-five card, the
resulting records are subject to generational degradation over usage,
especially when typical usage includes being carried in pockets or
school bags.  The ball-point pen (wide-tipped is my preference)
significantly reduces the generational usage loss, although it's not
immune to it.

Additionally, the tools that the broad classes of pencil/pen-like
utilities are compatible with tend to be incompatible with utilities
that I use to mitigate this generational loss, namely rsync, unison,
md5, sha256, and Git.  (I've heard rumors of prototypes that are
compatible with these utilities, but I've yet to see them personally.) 
Remember, there are only two types of computer users: those who've
experienced data loss and those who are about to.

While I do still stick with pen and three-buh-five for quick notes whose
longevity is not important or whose data is already stored redundantly
elsewhere, or as an alternative to LaTeX when I don't have access to an
input device, I've generally switched to LaTeX for subject notes which I
want to keep around for a while.  I do still use the three-buh-five
family of tools for early speculative design documents, though, since
the interface is much easier for spatially arranging thoughts.  (The
Gimp and PBrush are just not very user-friendly for things like
pressure-sensitive strokes or tactile feedback, at least not without a
lot of specialized hardware.)
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