Possibly. Perhaps Jensen is toasting in memory of Megan, or Motoko in honor of Hideo Kuze. Maybe Adam has Faridah (for those who left her in their gameplay) on his mind, while the Major is remembering the sacrifice of the Tachikomas during the Dejima Island incident. They have both gone through so much in their lives, lost so many friends, comrades, and loved ones, it could be any number of them. It's up to our imaginations to draw our own conclusions, really, just as envisioned .
I'm probably going to do the same... Once I have time to finish the game that is .
After all, why should the fate of the human race be left in the hands of a single, fallible man, even if he's a hero? Our lives are our own, and it is our choices in them that make us who we are, or are not. Something as big as human augmentation? We should have our say in how that is used, or restricted.
Don't get me wrong, I'm all for transhumanism and advancing the human condition, but still, we need to accomplish it through a joint effort, not by having our opinions swayed by some shadow cabinet like the Illuminati.