Randall:

I've got a couple of remote projects that I developed and now maintain.
 They are both running in a Winblows environment but I'm pretty sure
similar software would work with a Linux based system.

I am connected via VPN routers and use Timbuktu to control the remote
machines.  Timbuktu (while not my favorite) will do file transfers as
well so I don't have to run an FTP server on the remote end.

I do my file editing and compilation locally and send the jar files out
for test and installation.

The VPN keeps the connection and data secure (although in this case it
is really overkill).

One of the sites I have never even been to.

I would suggest that you get a subset of your large data set for local
develpment work.

For the Linux environment I've been playing around with VNC under SSH.
I think it is as secure as any SSH setup and seems to work great with
FC3.  Linux has good FTP servers and the combination would make it easy
to install and test remotely.

I really don't know anything about IDEs so I can't help you there.  I'm
a dinosaur and a year or so ago switched my text editor to VIM.  That
was a big change for me as I had been using Intel's Aedit for the
previous 20 years or so.  Before that is was EDLIN :-).