its best to find synergies. stacking any one thing isn't usually a best approach, with the exception of cooldown reduction
10% cooldown reduction with 100 dps through abilities= 111dps.
20% cooldown reduction with 100 dps through abilities = 125dps
40% cooldown reduction with 100 dps through abilities = 166dps
however attack speed works the opposite way, as does crit chance, damage, crit damage, etc... Those items are usually best used as a blend. 10% crit chance + 10% attack speed is better than 20% of either.
armor/magic pen can be a little weird, as it knocks flat amounts off of enemy armor. oddly enough, this matters most with lightly armored opponents. 20 armor pen will increase your dps by 20% vs a character with only 20 armor, but only 5% vs someone with 100 armor.
personally, I find mana regen runes to be essential in almost every game. they're my must-have, regardless of me building dps, defense, cooldown, or whatever.
hit point/mana runes tend to be cool up front (at least if you're getting ganked a lot), but barely matter past the first 10 minutes, as by then the HP bonus is trivial in relation to incoming DPS.