We don't know for sure what (or who) Bob meant when he said "two more to go," but his threat certainly has a foreboding sound to it. Since your question restricts the answer to only information received in Chapter 25, one must forget about what happens in previous (and any future) chapters. Tom Robinson was the primary object of Bob's hatred, and Atticus would certainly be the next in line for any kind of retribution. Since Tom is now dead, it seems that Bob may set his sites on killing Atticus. As for the final member of the twosome, who Bob has in mind is anyone's guess.
Bob was referring to Tom Robinson as the "one down" and to Atticus and Judge Taylor as the "two more to go", because they were the people who caused his public humiliation at the trial. We know he was planning to do something to Judge Taylor, because in the book they mention Bob sneaking around the Judge's house, but runs away when the lights turn on.
However, Bob might have went after Jem and Scout in attempt to hurt Atticus even more.
I think Bod Ewell was referring to Jem and Scout.
Well, in simpler words, the "one down" is tom robinson but the "two more" were Atticus and Some one else who might be some other negro or maybe Heck Tate.
I think that Bob Ewell mean't Tom was one. He wanted to get back at Atticus for actually defending Tom that if he tried to harm what mean't most to him which would be Scout and Jem. Which if he did that he would get back at Atticus for making a fool of him at the trial. That means Jem and Scout were the two to go