I used to consider pen(cil) & paper as the only medium worthy (and secure) enough for transcribing the ideas that popped into my young head, although now I use an iPad, a Bamboo stylus, and either Paper or Penultimate to record all my thoughts.
I think my preference for paper stemmed from a childhood experience I had with keeping my first journal on an old DOS/386 in a password-protected WordPerfect file (and I still remember that password! :-) Originally, my intention was merely to try to use up all the memory on that machine, but I soon had a fond habit of taking 15-30 minutes per day to write about the world around me. What I wrote would likely be mundane from an outsider's perspective, but there was a sort of innocent joy in noting all the tiny insights and observations I had that were important to me at that age.
One day, I went to update my journal, which was entitled MY LIFE, and discovered it and its backup had been erased from the drive. My father must have found this strange document that he could not open taking up loads of space on his computer and deleted it without a moment's hesitation.
I was devastated. I swore to never save anything of personal value to a computer again. I think this bad childhood experience actually engendered a deep technophobia that I harbored from high school throughout college and didn't really overcome until the last five years. This same experience also seems to be the root of a lifelong passion for writing.
In any case, I began keeping a more "formal" handwritten journal in the latter years of college up until a few years ago. It was written in pencil (preferably 0.5mm) on lined looseleaf paper contained in a large, unmarked 3-ring binder. I wrote in it daily, not really trying to distinguish "good" ideas from "bad" ones, but just concentrating on getting at least one complete thought on paper per day. Though I used pencil, I only erased obvious errors (like misspellings) choosing to strike through parts that didn't seem to fit at the time. I did this because when I looked back on what I wrote after significant periods of time, it often gave me further insight into how I had come about thinking what I was thinking at the time I wrote it.
It wasn't until about two years ago that I switched to using an iPad and a capacitive stylus for jotting down my ideas. Although it certainly doesn't have the same feel as working with pen and paper, I really like having a compact, infinite canvas to work with that I can take anywhere, and am reasonably confident that when the tablet grows up, it will transition from disrupting the PC to doing what it was meant to do in the first place — make paper obsolete.
In the event I get nostalgic for paper, I prefer using a blank 9x12 sketchbook — for the most part, I can't stand to be restricted by lines anymore — and my favorite Zebra multi pen:
http://www.jetpens.com/Zebra-Clip-On-Multi-2000-4-Color-0.7-...
Ultimately, I agree that paper is vastly underrated by geeks, but let's face it — after thousands of years, we're always trying to eye something better.
*Note: Safari quit unexpectedly before I could post this and I had to rewrite everything from scratch. Talk about coincidences!