If you want to do this form Win9x, you will not have a boot.ini file.
So, you can make a additional boot-up menu in your config.sys file
add lines in the beginnig of config.sys like the following:
[MENU]
MenuItem=WinStd,Standard Windows ShellMenuItem=WinGeo,GEO Shell
[WinStd]
[WinGeo]
;REM do not add this line
After that you shoul have TWO copies of the system.ini file - "system.in1" with Shell=Explorer.exe
and "system.in2" with Shell=C:\Progra~1\GEO\GEO.exe (or something like that - the *path* and the app you want to use like shell)
You should have lines like the following in your autoexec.bat:
@echo off
goto %config%
goto end
:WinStd
cd C:\windows
copy system.in1 system.ini
goto end
:WinGeo
cd C:\windows
copy system.in2 system.ini
goto end
:End
Rem This is the end line
Have fun,
Hope this stuff will help you,
Zlatin