For marks take armor penetration and magic penetration, because they pretty much cover for every champ. When you have more cash, attack speed and armor are also viable choices.
For seals, armor is your best bet. You can also take HP/level if you want tanky mage or you can take mana regen if you are running out of mana.
For glyphs, take MR/level. When you have cash, you can consider flat MR, AP, AP/level and cooldown or cooldown/level.
There is really no primary quints, so they are all good. But most used are movement speed, flat AD, armor penetration, flat AP, flat health...
For solo top, I'd take armor penetration marks, flat armor seals, MR/level glyphs and quints depend on champion, but flat health are pretty good for every champ.
For seals, armor is your best bet. You can also take HP/level if you want tanky mage or you can take mana regen if you are running out of mana.
For glyphs, take MR/level. When you have cash, you can consider flat MR, AP, AP/level and cooldown or cooldown/level.
There is really no primary quints, so they are all good. But most used are movement speed, flat AD, armor penetration, flat AP, flat health...
For solo top, I'd take armor penetration marks, flat armor seals, MR/level glyphs and quints depend on champion, but flat health are pretty good for every champ.

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http://www.mobafire.com/league-of-legends/build/rune-tips-what-secondary-and-primary-means-and-more-24255
This is a rune guide most of us tend to think is good. Should have like a "best buys" section.
This is a rune guide most of us tend to think is good. Should have like a "best buys" section.
AP Twisted Fate | AD Carry Kog | Support Sona
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I intend to solo top most of the time but since I won't be able to pick what position I want to play everytime, I'd like to know some cheap rune sets for some positions.
For solo top this is what I think will be useful:
- 9x Greater Mark of Desolation;
- 9x Greater Seal of Resilience;
- 9x Greater Glyph of Shielding;
- 3x Greater Quintessence of Strength.