The answer to this question is far more complicated than it seems. The choice that the doctor forces Sophie to make is between her son and daughter; he forces her to choose which child lives and which one will be executed. This is a heart-wrenching and seemingly impossible choice for a loving parent to make. Sophie is forced into making this choice, though, because if she refuses to choose one child over the other, the doctor will kill them both. While it is heavily implied that he would enact that threat, it is possible he may not have. Since Sophie does choose, she will never know what would have happened if she had done otherwise.
The repercussions of that particular choice influence each of Sophie's subsequent decisions. Since much of the novel is told through flashbacks, we can see how each choice she makes is influenced by her decision and the overwhelming amount of guilt that she feels because of it. By revealing the actual "choice" that Sophie makes so late in the novel, Styron provides an explanation for much of Sophie's character: her relationship with the abusive Nathan, confession of her past to Stingo, and finally another important decision Sophie makes towards the novel's end.
The novel's title, then, can refer to the many choices that Sophie makes, and this emphasis on choice leaves a lasting impression about the nature of decision. The novel reveals that each choice we make can ultimately impact both our lives and the lives of others, yet the decisions with the greatest impact are often made suddenly, without any thought towards consequence.