a) Marks (colored red): increase Attack and Damage statistics
b) Glyphs (colored blue): increase Magic statistics
c) Seals (colored yellow): increase Survivability statistics
d) Quintessence (colored black): super Runes which greatly increase stats
Few exceptions: Mana reg are better on yellow than on blue.
On reds you get magic penetration which is magical sorta
Somewhere in the guide section on page 1/2/3 there is a thread with a rune spreadsheet, you can search for it or manually find it. Gives a nice excel file with all the runes listed including what is best on what spot.