For me it would have to be Smith.
Jefferson is still a bit small (for my preference) at the center spot, yet he's too slow to play PF. His defense is sub-par. He's a very good player (and will continue to be for years to come) but I think we've already seen the best he has to offer, and I don't see any room for him to improvement. Jefferson gives us rebounding, interior muscle and inside scoring...but I think Sullinger can give us all that for a LOT less money.
Millsap is a really nice player, but I just don't see how he helps us with our current size predicament at the PF spot. At 6'8" he really isn't any bigger than Bass or Sullinger, and lack of height at that spot has been killing us ever since KG moved to center. Like jefferson, I don't think Millsap has much potential to improve past where he is. He can play both SF and PF, but he's not much of a shotblocker and I wouldn't want to see him at Center even if we got desperate.
Smith (at 6'9") gives us decent size at the PF spot, combined with Elite atheleticism and decent strength. He can score arouund the basket and outside. He's a threat on offense and on defense. He gets his share of steals, he's an excellent shot blocker, he's a very good rebounder, he's an outstanding passer. He has all the raw talent to be an elite superstar, with his mentality and environment being the only things holding him back...and that tells me he still has some potential to get better.
Honestly I'm not going to be upset with either one of these guys, but give the choice I'd have to take Smith.
Honestly, the odd thing is I'd probably take Gortat second. He's obviously not as skilled a player as Millsap or Jefferson, but I just thing he fills out needs better. He gives us size (that Milsap lacks), defense and athleticism (which Jefferson lacks), efficiency on offense (which Smith lacks) and a relatively modest contract (which all three of those guys will probably lack).
While these guys are all pretty young still, I believe Smith is the only one of the three who has still has the potential to improve. Millsap and Jefferson IMO have already seen their peak years.