Eclipse's remote target management is based around using ftp, ssh, or a custom daemon to copy files to the target, launch programs, etc. As I said, it's rather immature at the moment, and the custom daemon is not trivial to get running (I crosscompiled an SSH server instead...). Overall I gave up on it, though - I'm not interested enough in getting it working to bother learning Java in order to do it.
Ignoring the Eclipse RDP project completely, you could probably make a plugin to handle the launch via SSH - provided you've already launched the SSH server of course. You could use "expect" to do the same via telnet protocol but it's not as trivial. It's a shame gdbserver can't run in a daemon mode itself, allowing the remote gdb to specify the program to load and launch. I guess this is why the Eclipse project uses a custom daemon.
Personally I just use rsync to copy my files across, and the standard telnet interface in a separate window to launch the app. I usually just run it, only using gdbserver if I'm actually debugging. My telnet session tends to die when the remote gdb quits, which is somewhat awkward, not sure why (or how) it does that though.
(An interesting point about the QNX plugin for Eclipse is that it claims to have support for launching and debugging at the kernel level via JTAG... could be useful if we can get a free copy.)
I put some notes on using gdb and gdbserver on the wiki too, feel free to add to them if you think it would help. It's currently pointing at a precompiled gdb build I'm hosting myself but maybe it should point at the archive instead.
Getting gdbserver to support threads properly is tricky in statically linked programs, does yours support this? You need to build libthread_db statically, then gdbserver's configure should detect it and use it; then you can only debug programs linked against exactly the same build of the threading libraries. I was looking at getting the Open2x build scripts to handle this but got distracted.
If you're interested in any of the servers etc I've successfully built/ported for the gp2x, they're mostly on my web page here:
http://www.glost.eclipse.co.uk/gfoot/gp2x/