Attached to this post is a tool you may use to create Master System Lemmings levels, along with its source code.
The tool included is not an actual level editor. It simply copies the ROM, then "injects" the level you designed using Mappy into the copy. You may download Mappy at
http://tilemap.co.uk/mappy.php. Mappy is designed for Windows, but Linux users should be able to run it under Wine. It won't work on Macs, unfortunately. I need more programming experience before considering making a fully functional, portable level editor.
You can choose which level you wish to overwrite, but you can only overwrite one level right now. Also, the game will automatically modify some levels, such as Tricky 04, Tricky 21 (massively), Taxing 24, Mayhem 03, Mayhem 13, and Mayhem 27 (there are likely others). This is a "feature" of the game itself. I plan on updating this program to cancel these effects if you choose to overwrite those levels. Also, let me know if you find some others. That would be great.
One other thing, and it's about the use of Mappy. The tile size is 8x8, the map size is 112x19, and the tilesets you need to use are included in the zip file. After you've designed your level, you need to go to Custom -> Export binary file. When asked about adjusting exported values, set it to 0.
That's all I can think of right now. Let me know if there's anything you need help with. Hopefully nothing along the lines of "This program doesn't work" or "My computer burst into flames after running your program". That shouldn't happen.
[Edit: Oh yeah. Don't forget to modify the leveldata.txt file. It should all be explained in the readme.]
[Edit 2: Updated the program to allow .mlm files to be used, which uses the same file format as within the ROM.]
[Edit 3: Lemming maps for the original game now available.]