Does anyone know of tools (or IDE plugins) that could enable me to
conveniently launch and debug remote applications?

I'm a part of a team that develops processor-intensive and RAM-
intensive scientific applications, and our general strategy to date
has been this :

1) Develop a RAM or processor intensive algorithm on an individual PC
2) Try it out on the PC (unit tests, small data) to make sure it runs
3) Create a jar file
4) Manually upload the jar file to a high-performance server
5) Use GoToMyPC to test the application on the server

This is a laborious process, and  if something goes wrong on the
server, it's difficult to debug.  At one point, we used our source
control system to relay changes that the server would then check out,
build, and run.  But checking in "half baked" code to the source
control system interferes with the development process we have in
place.

Someone recommended that I consider using an application server like
Apache Tomcat, but I'd like a second opinion before I invested
significant time in this option.  I'm trying to avoid complexity and
execution overhead (I wouldn't want the system to severely affect the
performance of the application under test).

Any ideas?

-Chess