Ok, I've done some Tests and here is how my /home/user/test directory looks like:

drwxr-sr-x Incomplete
-rw-rw-r-- LimeWire
lrwxrwxrwx LimeWire.jar -> /opt/LimeWire/LimeWire.jar
lrwxrwxrwx LimeWire.lax -> /opt/LimeWire/LimeWire.lax
drwxr-sr-x Shared
lrwxrwxrwx collections.jar -> /opt/LimeWire/collections.jar
-rw-r--r-- gnutella.net
lrwxrwxrwx jre -> /opt/LimeWire/jre/
lrwxrwxrwx lax.jar -> /opt/LimeWire/lax.jar
-rw-rw-r-- limewire.props
lrwxrwxrwx swing.jar -> /opt/LimeWire/swing.jar

/opt/LimeWire and subdirectories are owned by root and it runs without any changes to permissions.
Remember that the startscript 'LimeWire' has to be in the directory directly,
doing a 'ln -s /opt/LimeWire/LimeWire . ' doesn't work.