One of the biggest reasons to go with a non-php solution is that it will avoid the default upload limit (100M is too big for it).
As far as the lowest usage, I can't tell you for sure. The applet solution does not sound like a great idea as not everyone allows applets to run. The server side question there is what is used on the host side to support the transfer.
There are some decent perl solutions that should not be very painful but I've not used any of those.
Someone should be able to come along and have more definitive information.
Or you could always install, measure and report the results...