At the time of the original trilogy's release, having seen Return of the Jedi, it seems obvious that Yoda is speaking about Leia, but there is now some debate. The debate has arisen because it was assumed by many that the way Obi-Wan had said of Luke "that boy is our last hope" indicated that he did not know who, or how important, Leia really was until that moment. However, as we see in Episode III, Obi-Wan not only knew of both twins, but assisted in their birth. It would seem strange that Obi-Wan might have forgotten her, or been unwise to her potential. Without the prequels, there is no doubt that we, as a viewer, could safely assume Obi-Wan did not know about Leia and Yoda's line "there is another" was a revelation about which he learned more in time to explain to Luke in the next episode. However, as with many plots, the prequels have altered our perceptions. Creator George Lucas has often stated that the movies are now designed to be viewed in order, 1 to 6. Watching the saga in this order, taking into consideration the Jedi "chosen one" prophecy and the eventual outcome of the story, another option could be that Yoda is actually speaking of Anakin/Vader, and some lingering hope that he may yet fulfill the prophecy. However, this seems a little ambiguous.
One can, and probably should, conclude that Yoda was making reference to Leia, despite Obi-Wan's seeming lack of faith in her. It can be taken as an indication of Obi-Wan being either pessimistic of their chances in light of the time and energy thus far invested in Luke, or of his desire not to involve Leia. But even with all this considered, strictly from a film-making point of view, the line was actually written to make audiences believe there was a chance that Luke might be killed by Vader and to therefore give their duel more tension. At the time that Empire was written and released, Leia was not meant to be Luke's sister. Luke instead had an unnamed sister, also undergoing Jedi training, on the opposite end of the galaxy. It is also possible that had Luke fallen to the Dark Side, then it would stand reason that Obi-Wan wouldn't want to get Leia involved, as both her brother and father had fallen to the Dark Side. Therefore there would be too great a risk that Leia herself would be turned to the Dark Side as well.