Wow, that's a great question. There's quite a few episodes that don't really seem to mean that much to me in title but when I watch I am reminded they are so much more.
I would probably list:
Convention, Surgery, Malcolm vs. Reese, Charity, Monkey, Hal Grieves, Hal Sleepwalks, Butterflies, Malcolm Holds His Tongue, Academic Octathlon, and most of season 5, which many people say was the low point of the series.