Personal favorites of mine include:
The battleship/train stages in Raiden Fighters 1 and 2 - The frantic left to right (and vice versa) scrolling that occurs when I am trying to destroy different ship/train compartments really reminds me of the fact that I'm fighting against a behemoth against all odds and always makes me feel uneasy regardless of how well I'm doing.
Stage 6 of Biohazard Battle - It looks like a "normal" giant aircraft at first, but after you dismantle the first section you realize that it's a "living" ship with its disgusting organs exposed and odd extremities growing out of it.
Stage 3 of Mushihimesama - This level is a classic and will always draw me back to the game regardless of the fact that I like the sequel better. Each different section of the level is just a blast to play through.
So what are your favorite "dismantling" levels?
Yo dawg, I herd you like bosses... ok I'll stop now
