The Emancipation & E=MC˛ are by far and away her best albums.
Not only are they amazing, but the eras were great in hindsight -- her confidence was high, she was slaying the younger girls, yielding #1's back to back, doing 400K first weeks, and had great performances (compared to Glitter & Charm, and her Memoirs / Elusive performances).
I also love the fact E=MC˛ is like a Pop Version of Emancipation. Emancipation is her best R&B oriented album, and E=MC˛ is her best Pop-leaning album.
Shake It Off, We Belong Together, Say Somethin', Don't Forget About Us, To The Floor, Fly Like a Bird, Mine Again, Stay the Night, etc. >
Touch My Body, I'll Be Lovin' U Long Time, Last Kiss, I'm That Chick, Cruise Control, Love Story, 4Real 4 Real, Migrate, etc. >