Now I'm curious. From an archival standpoint, wouldn't a pencil be better than a pen unless you're using some really high quality ink? I find that ink degrades much faster than graphite when it is exposed to light and moisture.
India ink is a good solution to this problem. Koh-I-Noor Rapidograph pens are good for this application because they have a nice mechanism for breaking through dried ink on the tip of the pen. Even a ballpoint pen is quite good for being moisture resistant, although I don't use them so I don't know much about fade resistance except a guess that black is best.
The idea of not using a pencil is to prevent changes later. It's really important not to make changes that cannot be tracked. The best is to cross out, write in new text, and sign+date in the margin. Leaving lots of space helps in this. Frankly, though, I've seldom found small changes. When an analysis turns out to be wrong, I simply make a new entry. With my forward- and backward-referencing notation, it won't matter if the new entry corrects an error later in the day, or a decade later.
I've never worried about sunlight because my books remain closed on a shelf, when not in use. As for water, choosing a good ink helps a lot (even my fountain pen scrawls can resist quickly-dabbed-up tea stains), but making copies/scans is really a great solution.
An addendum to my earlier post -- it helps to title each entry (which often corresponds to a day or two of work), and to type those entries (plus dates, book number and page number, and also some keywords) into a file that can be searched. I recommend one line per entry, and a format that is uniform enough that you can use grep (or similar) actions to produce specialized tables of contents for individual projects, years, etc.
