Uninstallers worked by keeping a log of changes when an app was installed. There are no logs at this point, so it would be pretty useless. Delete the directory of the program you want to get rid of. Open the autoexec.bat and config.sys files one at a time in a text editor (even the DOS edit app will work). Find any entries that look like they might belong to the deleted app. Instead of deleting the entries, put the letters rem and a space in front of the line. This is called "commenting out" lines. It is good because if you accidently remove something you really needed, just remove the rem and space to restore it. You can comment out lines in the win.ini and system.ini by adding an apostrophe and a space at the beginning of the line.
There is no registry in win 3.x. Talk about uninstallers, I remember when few programs had an INSTALLER. Make directory, copy files, manually add entries to the autoexec.bat and config.sys files; including irqs, dma channels, and i/o port values to match the jumpers on your hardware. Used to be fun just setting up games. Different drivers for every screen res lol.
Linux may run fine in a command line mode on the rig, but a current GUI might choke it.