First, the programs would have to support Win2k. Then what you must do is create shortcuts, or manually input all the information (pointing to the program already installed) in your Start>Programs>, and list the programs you want to be available in Win2k.
Or the easer way would be to do a clean install of WinME and Win2k, installing program you want for WinME on ME, and installing programs you would want for Win2k only on Win2k.
Actually it may be shorter to do it the other way, but you may run into some problems.