[Elladan and Elrohir]

I've always understood them to be Orthanc and Cirith Ungol, just because that's where the story takes you, and that's what Tolkien said.

But I'm beginning to think it could be Minas Tirith and Barad-dur. After all, in Book II, Chapter X, the chapter that can be considered the prelude to TTT, Frodo looks from Amon Hen and eventually focuses on Minas Tirith, and the greater and stronger tower set against it. This has been erroneously identified as Minas Morgul by at least one person in this thread, but it is clearly Barad-dur. So in that chapter, the Two Towers are clearly MT and BD.

We must keep in mind that Book Three is Secondary Action and Book Four is Primary Action (the Ringbearers and the Quest proper). Thus, especially with the chapters dealing with Faramir, I can see how The Two Towers could refer to Minas Tirith and Barad-dur.

But by no means have I reached a conclusion on this. At this point, my top five picks are:
1) Isengard and Cirith Ungol
2) Minas Tirith and Barad-dur
3) Isengard and Minas Morgul
4) Isengard and Barad-dur
5) Minas Tirith and Minas Morgul

But I am willing to be convinced, if anybody has anything I haven't thought about yet.