Marks is pretty much your choice. Depending on the champion, you should get either MPen or ArPen (shen and amumu would get MPen, rammus would get ArPen).
Seals can be either dodge or armor (dodge might work against a champion like amumu, who gets a benefit from being hit - his cooldown on
Tantrum is reduced).
MR would be best for blues, but if you have a mana-thirsty champion you want to play (malphite, for instance), then mana seals might be nice (though you could just get mana per 5 seals instead).
Quints would be anything you want - flat health is the best universal choice, but there's seals for everything.
Seals can be either dodge or armor (dodge might work against a champion like amumu, who gets a benefit from being hit - his cooldown on

MR would be best for blues, but if you have a mana-thirsty champion you want to play (malphite, for instance), then mana seals might be nice (though you could just get mana per 5 seals instead).
Quints would be anything you want - flat health is the best universal choice, but there's seals for everything.
Trojan and Jebus are absolutely right. If you have more questions about runes I'd suggest using this resource: http://www.mobafire.com/league-of-legends/build/rune-tips-what-secondary-and-primary-means-and-more-24255

Thanks to GrandMasterD for my sig!
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