The way it works (roughly) is that if your crit chance is <50% for the portion of the game where you want to maximise your dps, crit chance runes are better. If on the other hand it's >50%, crit damage runes are better. I focus on gold/5 and farming up until roughly the 15 minute mark, if people are stupid enough to let me score a kill all the better. Mid-late is where I want to do damage. I've tried penetration and AP builds and I just don't find them to be as effective as the crit build plank.
I run crit damage runes and my build usually goes
another avarice (if before the 15m mark)
then sell off the philo and avarices for desired items as the game progresses. Grab boots 2 whenever you feel the need, it's a gut call, but if you can delay them as long as possible you ramp up significantly quicker, it just depends on the matchup.
My most recent game ended with Last Whisper, Malady, Bloodthirster, Trinity and IE at 15/13/20. Truthfully I'm not that experienced with plank and the late game items could've went better (switch malady/blood for guardian for example).