The following levels will require either removal, replacement, or a large degree of modification (minor modification isn't included in this list):
LP1 (22 levels total)
Funny2) In The Long Walk - Beach graphics set
Sega Six - Custom graphics set
11) LEMMING INSANITY! - Special graphics
16) The Commander Keen Level - Special graphics
Strange5) Lemmdows 2000 Professional - Special graphics, vertical scrolling
7) Let's Play Triple Triad - Special graphics, vertical scrolling
12) The Weapon Room - Beach graphic set
15) We All Fall Up - Upside down
Weird3) Lemmings In The War - Custom graphic set
9) A Holiday In Hell - Beach graphic set
12) The Writing On The Wall - Special graphics
13) Sega Seven - Custom graphic set
15) Sega Eight - Custom graphic set
16) Poor Wee Creatures War Remix - Custom graphic set
Wacky1) 9R33N L3MM1N95 - Special graphics
12) We All Fall Up XP - Upside down
Insane1) Get in your car, and drive up the wall - Special graphics
2) Are You Keen? - Special graphics
3) Lemmdows 2000 Server - Special graphics, vertical scrolling
4) Card Time - Special graphics, vertical scrolling
This Is Not A Test - Special graphics
9) Yeah Lemma! - Special graphics
LP2 (13 levels total)
Light15) Indirect Route - Vertical scrolling
Neutral5) Confusion - Vertical scrolling
10) Just Go Up - Custom graphic set
Dark2) Quick Clicks - Release rate is above 99
4) Just Get Your Lemmings There! - Beach graphic set
10) Goin' For It - Custom graphic set
11) The Ghost Floor - Cheapo mechanics
13) Oblivion - Cheapo-exclusive terrain pieces are vital to the design
15) Temple of Oblivion - Cheapo-exclusive terrain pieces are vital to the design
Evil A Miner Problem - Cheapo mechanics
9) Castle of Oblivion - Cheapo-exclusive terrain pieces are vital to the design
11) Race of Insanity - Custom graphic set
13) Quick Clicks II - Release rate above 99
LP3 (13 levels total)
Daigoro Forever Seven - Cheapo mechanics (although they're not essential, but the lack of them would be a huge annoyance in DOS)
15) Lane of Lament - Cheapo-exclusive terrain pieces are vital to the design
Kozuka5) Sunrise - Special graphics
7) Lane of Lament - Cheapo-exclusive terrain pieces are vital to the design
Wakizashi Sunrise II - Special graphics
9) Lane of Lament - Cheapo-exclusive terrain pieces are vital to the design
19) Copyright Infringement Part 1 - Possibly too wide
Zanmato1) Lane of Lament - Cheapo-exclusive terrain pieces are vital to the design
4) Copyright Infringement Part 2 - Possibly too wide
6) Sunset - Special graphics
Impulse of Light - Cheapo mechanics
9) The Way Across - Cheapo mechanics
11) Down The Middle We Go! - Vertical scrolling
That's a total of 38. However, some of them (Oblivion is the first one to come to mind) could be reconstructed in DOS using alternative but similarly-functioning designs, or possibly even different graphic sets that do have the required pieces. Should this be done by combining the packs, the Lane of Laments would be likely candidates for removal due to the terrain similarity (and in one of them, solution similarity) to Oblivion.