What does Kirito say at the end of SAO?
From the corresponding scene in the light novel (volume 4, chapter 9; p. 308):


  キリトは透き【すき】通った視線で一瞬【いっしゅん】アインクラッドを見つめ、しばしうつむいた。その唇【くちびる】が動き、かすかな声で誰かの名前を呼んだようだったが、聞き取れなかった。


Translated,


  With his penetrating gaze, Kirito glanced at Aincrad for a moment, and then cast his eyes downward. His lips moved. It seemed as though he had said somebody's name in a faint voice - but [Yui] couldn't hear him.


In light of this, it is clear that Kirito said somebody's name. It seems, however, that the author chose to leave the identity of the person ambiguous. 

I believe that the standard inference among the SAO fanbase is that Kirito said either Sachi's name or Kayaba Akihiko's name. This seems like a reasonable guess to me, though I'm not sure if there's any other evidence supporting it.