Definitely the Mothership in MS3. It's not that the enemies are hard to kill (Not counting the boss before the Clones- EVIL!), it's just that it's such a long level, and that the old phrase "Strength in Numbers" is taken to a whole new level with the Spider Bots. And for them, there IS honour in death. For you, there is not.
Honourary mention goes to the first half of the last mission in MS1... Until you figure out the easiest way to do it- At the start, inch across the screen very slowly, killing any soldiers, so that the screen doesn't move, but you can see the Tank. If you keep your distance, the Tank won't actually "see" you, and won't fire. Destroy it, find the secret hostage that gives you a weapon, and continue to advance slowly, taking out anything quickly. Well, that's how I do it anyway.