I am currently using this method, Faction > Card Type > Cost (Descending), in a box. For me, I think a binder would be much faster to find cards, than rifling through horizontal cards in a box, even when I know where the cards are. Also, the cards are much safer and would receive less wear from removal and replacement in a binder, IMO.
@striatic My idea was to get several of the Ultra Pro binders, maybe 1 Runner and 1 Corp. Your option is more economical, but in my experience, the larger the binder, the more susceptible the pages are to damage, especially when the binder is very full and flopping around. Does the binder you linked have hard or soft covers?
Besides the reasons stated above, I am leaning towards a binder because
A) Netrunner has killer artwork -- the best around, IMO.
B) A binder would be more accommodating and more appealing to show to new players
C) Easier to rediscover cards you'd forgotten about when flipping through. Inspiration!