Homeworld, the last level.
Not very difficult in itself, but your fleet carries over from previous levels. If you didn't do to well on that mission (Read: Know exactly what you would need in the next level), you would basically be screwed for the last level. Of course, my screwup on the third-to-last level meant I had to restart all the way back there to have a shot at the last level.
Wing Commander Prophecy: Secret Operations
Basically the whole add-on, but one level in particular.
You've got five wingmen on every single mission, to fight three dozen enemy ships per battle (usually 2 or 3 battles per mission). Not just regular ships, but 5 or 6 Stingrays. Now, for those of you who don't know WC

(consider yourself lucky), Stingrays are horribly scary. The final mission of Prophecy had two stringrays, and in the add-on, you face half a dozen on a regular basis. Needless to say, I still don't know how it ends.
ultra_v_89 said:
The driving section of Battle Toads, proof there is a god, because there certainly is Satan, from whom elses ass-crack could such a level be crapped out? I didn't get many games as a child, how fortunate to receive one with only two possible levels.
Agreed. I only beat that level when I finally played it on an emulator, with a "Save state" button. And it still took me about 88 quicksaves.