PokerTracker

From what I gather, equity_allin() is a function that just tells you what your equity was at the moment someone went all in.

Is there a way to figure out what your equity was on the pf/flop/turn/river, as they are displayed in the replayer?

In PT3 you can only see those values on the replayer. In PT4 we have a built in equity calculator that you can use to calculate your equity in any variety of spots. It's available via Tools -> Equity Calculator.