I found a very nice way using Meld. Meld is a graphical comparsion tool and will work very well as an external tool of gEdit:
1) Install the package "meld"
2) Start gEdit and opening the Menu "Tools > External Tools..."
3) Add a new external tool:
* Name: Compare Files
* Description: Compare then opened file with another
#!/bin/sh meld $GEDIT_CURRENT_DOCUMENT_DIR/$GEDIT_CURRENT_DOCUMENT_NAME `zenity --file-selection --title=File for comparsion --filename=/home/` &* Any othe roption is not interesting so press close
4) Now you have in "Tools" an menu entry "Compare Files" that will use the active document of gEdit and the other browsed file for comparsion