I know this thread is just for talking about the Amiga and DOS version, but if you extend the list of candidates to the rest of the different ports of the first game, there is an unanimous winner for the hardest level ever, and I'm sure it is "I Am A.T.", followed by many of Present and Sunsoft levels.
Nope. The Mac's version of "The Steel Mines of Kessel" beats that by a mile. (It's the same as the Amiga version, but since you only get 80 lemmings and the original game runs on percentages, you can only afford to lose 8,
and three of the thorns on the final slope before the trap turn back the lemmings when they're not meant to, thanks to the Mac's high-res graphics, so you have
more obstacles where bombers are needed.)
Anyway, for this thread I agree we should decide on one version of the game to judge by, since if we include multiple versions we leave ourselves open to someone pointing out yet another version we haven't considered. And that means Amiga or DOS, pick one. You can't lump the two together when so many levels differ between the two:
* Lemming Drops / Have a nice day: As pointed out, the lack of water makes this easier on DOS.
* The Fast Food Kitchen: An infamous example. DOS relaxes the time limit and save requirement so much that it's easier than its repeat.
* The Steel Mines of Kessel: As Flopsy mentioned, Amiga gives you 10 of each skill and 90%. DOS gives you 20 of each and 75%.
* Come on over to my place: Requires 100% on Amiga (and Mac), 80% on DOS.
* Just a Minute (1 and 2): I know the Amiga is one of the versions with a fast game clock so you have less effective time, and fewer solutions will work. I think the DOS version is more relaxed than the Amiga, but less so than the Mac? Not entirely sure.
Anyway, at a glance, it looks like most of the really hard levels have been mentioned by now, so I'll just give my votes for the top 10. (This would be easier to do for ONML. I still have the book in which I wrote down all the access codes for both games, but the Lemmings ones were copied from an earlier list, so they are all done with the same pen except for those after The Steel Mines of Kessel. In the ONML list, there are several changes of pen that mark where I got stuck for a long time.)
(0 - The Steel Mines of Kessel, but on Mac, so that doesn't count)
1 - Save Me
2 - No added colours or lemmings
3 - POOR WEE CREATURES
4 - Triple Trouble
5 - The ascending pillar scenario
6 - Come on over to my place
7 - Steel Works
8 - Compression Method 1
9 - I have a cunning plan (yes, this is trivial with the blocker release trick, but you don't find that out until much later in the game)
10 - Postcard from Lemmingland