The library was my favorite, so classic. It is right above the Hellmouth. I loved it from the first moment (Giles slamming down the Vampyre book) to the last (blowing up the Mayor in the library). Giles: "I'm just going to stay and clean up a little. I'll be back in the Middle Ages." Jenny: "Did you ever leave?"
The Magic Box is my next favorite. All the great stuff there, the cool training room, the balcony (the dark books, remember Tara singing on the ladder in OMWF and the gang sitting up there in Checkpoint?), the basement with the mummy hand LOL.
Giles apartment has some funny memories: Spike in the bathtub, Giles: "Xander, don't speak Latin in front of the books", drunk Giles & the gang fighting in The Yoko Factor.
Buffy's house is my least favorite, as least from a Scoobies headquarters POV. I love the house in general: roomy but cozy. I do love the Scoobies hanging out there in Restless & part of their dreams occurring there, and I love the Faith & Buffy dreams in Dawn's future bedroom.