The basic runes someone should have are
Quints: Flat HP, Flat AP and Armor Penetration
Marks: Armor Penetration, Magic Penetration (and also Flat Attack Speed if you jungle)
Seals: HP/Level, Flat Armor (and Dodge for those champions with innate dodge such as Jax, Nidalee or Sivir)
Glyphs: Flat Cooldown Reduction and Flat Magic Resistance
MP5/Level seals aren't all that great anymore due to its nerf, so the increased mana regeneration is pretty negligible. It would be a better investment to use HP/Level or Armor seals as they increase your survivability. Between these two runes, it's based on your personal preference.
Casters would generally have
AP or HP Quints, Magic Penetration Marks, HP/Level or Armor Seals (I prefer HP/Level) and Cooldown Reduction Glyphs.
As for AD Carries, I would get
Armor Penetration Quints and Marks, Again, your choice of the two Seals but I like Armor, and Magic Resist Glyphs.
Remember that Runes are made to compliment a player's playstyle, and so you should customize them to fit how you play.