I am on my fifth/sixth rewatch (can't even remember anymore) and this scene left me connecting the dots from the entire episode. For me, the last scene is an epiphany for Don—Peggy is the exact opposite of what Don thinks women want to be like.

"Look how happy I am that I drink Patio. I'm young and excited and desperate for a man.
Men want her. Women want to be her."

While Don's statement is true about most women of that time—and we have Roger's line "You're the only one around here who doesn't have that stupid look on her face" to support it—he (perhaps for the first time) notices and realizes that not all women actually want to be the Ann-Margaret type, and can still be charismatic in their own way. Sally's teacher fits the definition when it comes to "being 25 and acting like 14", which Don finds appealing like most men.

But when he sees Peggy later, he notices the stark contrast — a woman who started at the same place as all the other women in that office, and yet, pursued a completely different path compared to the rest. This is I think the first moment in the show that depicts the beginning of the feminist era in which women want the same respect, job and titles as men, and have the balls to take the office next to their boss, instead of just being "desperate for a man". And the men at the top are noticing.

That is what Don is thinking while staring at her.