Hey,
I have an emulator for windows games configured as follows:
Emulator Name: Windows_Games
Executable: cmd
Command Arguments: /c "[romfilename]"
rompath: ..\..\roms
rom Extension: .lnk;.bat;.cmd
System Identifier: PC
Obviously, change the "rompath" as you need to!
Put your games in subfolders of your rompath and create shortcuts to the exe files (or batch files if you are feeling fancy)