Quints: Flat health bonus are great for everyone.
Red: You'll need two types here: Magic Penetration and Armor Penetration. The first one is useful for more champions, though.
Yellow: Dodge and Armor (flat or scaling) are reasonable for everyone. Mana Regen is great for all champions that use mana.
Blue: Cooldown Reduction and Magic Resistance (flat or scaling) are useful for almost everyone.

Your guess is right. Scaling runes catch up with flat runes at level 9 generally. From there on, scaling runes are better.

Personally, I'm more inclined to use flat runes. I believe that the part of the game that I most need those bonus is in the early game, as late game I'll already be well equipped anyway. But many players prefer to use scaling ones.

I believe you could start with the flat health Quints. Those are really universal runes, since they really improve the early game of every single champion.

Your choice deppends on what champions are you playing, tell us, we could help.

For reds:

Armor Pen/Magic Pen/ Attack Speed

For yellows:
Mana Regen/lvl HP/lvl Flat Amor

For Blues

Mana Regen CDR AP/lvl MR

For Quints

Flat HP/ MS/ARpen/Flat AP


http://runeterra.com/forums/index.php?topic=1137.0

If you're not playing a tanky character and you want extra mana regeneration (always a good thing), the tier 3 seals and glyphs of mana regeneration per level are the way to go. Combined they give about 27 mana regen per 5 seconds at level 18, and break even with the flat mana regeneration version at about level 5. They're also really cheap for what they do.

the yellows are the primary and the blues are the secondary, but the difference is 1.8@18 vs 1.44@18.