hi m^(2),
i tested junction using the command line ln.exe by Hermann Schinagl and its working great!

this is just another alternative to save space, i was thinking of a common files(libraries) folder, similar to portableapps common files folder but we will use symlink/junction so that other program can use it aswell, here you put all your common files like dlls, java, gtk, or any file that other program may also use, this will minimize duplicates, saves space and you can centralize the updates for dlls, java and other common files.
i just use java as an example using junction, you can symlink specific dlls to apps as needed, haven't tested it though, but i think it should work.
Example for Java
Common Files/Common Libraries
-Java (size approx 86mb)
OpenofficePortable [portableapps]
-App
-Java [Junction] (- 86mb)
X-Jampal_1.23_rev7.zip [winpenpack]
-Bin
-Lib
-Java [Junction] (- 86mb)
Freemind [app that needs java to run]
-App
-Java [Junction] (- 86mb)
the problem with this approach is at first you have to replace files to symlink/junction.
it would be easier if it can be automated with a gui.
cheers