Does anyone know/remember how exactly the Steam holiday sales work? Can games that are on sale but not in the "today's deals" section get a bigger sale later (by being part of a "today's deal")?
Yes, that can happen. So for the general sale I'd recommend waiting until the last days with buying something so you don't accidentally buy it before it becomes a daily deal.
So yeah, if for whatever reason, despite having had a billion discounts already, you still don't have Deus Ex, get it now. It's cheaper to get both games together then just DX1 so go for the bundle.
Titan Quest Gold and Portal are also nice.
And the Sands of Time Prince of Persia games. But forget about The Forgotten Sands.