Molten Core didn't excite me much as doing Karazhan in BC. It was the first raid I really enjoyed. The storyline, the boss fights very exciting and truly memorable.
Oh man, so many great memories but the one that stands out was earning The Undying achievement and title with my guild in Naxxramas. We had a few close-calls that night, but we pulled it off and the cheerful screaming in voice chat still rings in my ears.