The title of the book is likely, at least in part, a reference to the Seanchan towers, which are mentioned a few times in the novel:
One of Egwene's dreams involves 13 dark towers, falling over one by one. While this is also a pretty obvious references to the Forsaken, the actual towers she is seeing are likely a reference to those in Seanchan.
There's a fragment of the Prophecy of Shadow at the end of the novel, which includes the line:
Yea, and the Broken Wolf, the one whom Death has known, shall fall and be consumed by the Midnight Towers
- Slightly more meta, there are 13 Towers of Midnight and this is book 13 in the series :)
As far as what the Towers of Midnight actually are, the only information we have are those few brief mentions and some additional information that eventually made its way into the Towers of Midnight glossary, and some things mentioned by Jordan at one of the DragonCons. It's notable for being a key base of operations while Luthair Paendrag was conquering Seanchan, and for being where he imprisoned the Aes Sedai that invented the a'dam.
They are current unoccupied, until such time as the imperial family of Seanchan decides to
return to the Towers of Midnight and "right that which is wrong."
That doesn't mean that the title is only referring to the Towers of Midnight in Seanchan; likely the title has multiple meanings. The other obvious reference is to the Black and White towers, and the Tower of Ghenji, since we see significant plot advancement on all three fronts.