In order to best preserve your writing in a journal, which is the best medium to write with - pen or pencil?
Does pencil last the longest on paper?
Does pen prevail? If so, does the variety of pen matter or the type of ink?
In my experience, pencil fades much faster than pen, on any type of paper. Pages rubbing in a journal cause pencil to get fuzzy, and it gets pale pretty quickly (I’m thinking of even the course of a semester - notes at the beginning of the semester look worse than those at the end).
As for which pen is best, or which type of ink, I wouldn’t know. Something tells me that black ink will at least be legible longer, but I could be totally making that up.
I don’t know about pure aging, but I would avoid fountain pens and flairs because their inks aren’t waterproof. I once dropped a notebook in a puddle a few weeks before finals… If it had been in ballpoint, I could have still read the notes after careful prying apart and drying. Since I used flairs, well, I had blotchly tinted blank pages to study from. 
Yeah, I know you don’t intend to drop your journal in a puddle. How about the time you knock over that drink?
If you want archival-grade permanence, load up a fountain pen with India ink. That stuff seems to last through just about anything.
No, no, no! India ink will DESTROY your fountain pen – it contains lacquer or something. Fountain pens should ONLY be used with water based inks.
If you want to use India inks, you have to use a dip pen, like a metal nibbed one or a glass pen.
My great-grandfather kept a journal in pencil during his two years with Stuart’s Cavalry during the Cival War. I have it. It is perfectly legible (people had good handwriting in those days, too).
I keep a journal in my computer. Barring electromagnetic anomalies or physical damage to the computer, the files’ll last for pretty much forever :D.
But I also write a lot with pencil and notice that it does fade in frequently-used notebooks. No fading if I write a little note and then dump it somewhere where I won’t peruse it for a while.
Sorry about the typo in Civil War. The journal is a cheap notebook that Grandpa wrote in whenever he had the chance – I’m sure he stuck it in a pocket & took no special care with it. A lot of his letters home also survive – also in pencil.
My chem teacher had us use pencil in our lab books because it was less susceptible to reacting with any chemicals we might spill on the pages. I guess graphite’s good for that.
So, whats the MTBF on your harddrive? 
I have some old WordStar files for you!