Depending on your resources and needs you can optimize your pages from there.
For example, AS reds vs AS quints. Quints are more efficient but jungler's use AS reds because they can put MS quints in for roaming (there aren't MS reds) Sometimes a champ scales good with health so someone like my brother runs AS reds, hp/lvl yellows, Armor quints and 3 mr 6 sc. cdr on his Skarner page because that's the best setup for his type of skarner (he doesn't get many cdr items so he runs them on runes)
I recently re-organized my rune pages http://na.op.gg/summoner/userName=LostFr0st
What you do is go through your champ pool and list your "for sure" champs and your "maybe champs," you then cross-reference them with these two sites
http://www.leagueofgraphs.com/champions/runes/skarner/jungle/all
http://champion.gg/
and figure out all of the possible optimal rune pages for all of your champs if you had unlimited runes and pages.
The next step is to put a star next to all of the ones in your list that you know you'll need and then fill the rest of the pages with 'edge cases' that you might need that are different enough from those pages to get their own page.
It's a lot of work but I've found it to be worth it in the long run.
Make sure you plan out your page order on paper and organize them by what reds they use to make them easier to find in champ select.
I'll probably go through mine again soon since I've bumped into a couple edge cases that I want to swap out due to champs I've picked up.
You'll likely have to do the same every few months.
Hope this helps ^-^