Here is how it works: I used Fielding Independent ERA from Fangraphs. But first I used RSAA or "Runs Saved Above Average" from the Lee Sinins Complete Baseball Encyclopedia. It adjusts for the league average and park effects.
Take Pedro Martinez, for example. He had 2,827.33 IP and an RSAA of 496. So he saved about 1.58 runs per 9 IP. Suppose we are in a league that has an average of 4 runs per game. It means he would allow about 2.42 runs per game.
But, according to Fangraphs, Martinez had an FIP ERA of 2.91, .02 lower than his actual ERA. So I subtracted .02 from 2.42 to get 2.40. Below is the top 25 pitchers with 2500+ IP from 1876-2011.
I also used relative runs allowed. Martinez, for example allowed 1006 runs in his career. Since he saved 496, that means the average pitcher would have allowed 1502. Since 1006/1505 is about .67, I gave him about 2.68 runs allowed per game (since .67*4 = 2.68). But then I lowered it by .02. To get 2.66. Here are the top 25 using the relative method