It all depends how you access the other machine. The simplest would be an NFS mount, and the use of find, with the -exec option.

Another simple way would be the use of rsync, which produces a list of files it downloads. You can read the output of rsync in a pipe, and then run each Java program.

FTP would be harder. You'd have to browse the directory tree yourself, checking all time stamps, and downloading the files you are interested in, which you then can run as Java programs.

HTTP would even be harder, because it's often not possible to browse, or to get timestamps.

UUCP could be an option as well. Just execute remote commands, wait for the results to come back, decide what you want to have, send more remote commands (to pack a file), fetch it, unpack, execute Java.

cpio could of course be an option as well. Or mail. Or samba. Or sneakernet.

-- Abigail