I like both chapters equally so this is a tough one to call. On the one hand, On A Rail has some great battles between the grunts and the vortigaunts. It's also probably the most labyrinthine chapter in the game with a whole load of areas to find if you leave the train. I got totally lost the first time I played it so I hated it for a while.
[m]Blast Pit[/m] was the first thing I ever saw relating to Half-Life, waaay back in 1998, about a year before I even got the game. It blew my mind and the scale of the tentacle when it reaches in and grabs the scientist scared the crap out of me. The one thing that let's the chapter down is the backtracking. Getting back up to the control room is tense the first couple of times, but now it's just a slog.
Incidentally, On A Rail was the second thing I ever saw relating to Half-Life, moments later.