It's hard to choose just five, but anyway:
Arcana Unearthed (I may not be a fan of everything in this book, but I love how Monte did the magic system)
Eberron Campaign Setting
Expanded Psionics Handbook
Faiths and Pantheons (I'm not a big fan of FR, but I love its cosmology)
Manual of the Planes
Though I do also really like Races of Stone, Book of Vile Darkness, Sharn, Draconomicon, and Complete Warrior.