Rust in Peace for me as well. Master of Puppets has some fantastic songs, but I think a couple of songs on there kill the momentum a bit (The Thing ..., Leper Messiah). The "less-than-fantastic" songs on Rust in Peace don't feel the same way. Then if I pick, say, four favourite songs from each album, these will be:
Master of Puppets: Title track, Orion, Welcome Home and Battery.
Rust in Peace: Holy Wars... The punishment due, Hangar 18, Tornado of Souls, title track.
When comparing these two groups, I find that I enjoy the latter just a little more.