Im using Eclipse PDT(Ubuntu 10.10) for web development and successfully uploading changed files with Rsync manually.
~$ rsync -e ssh -av /home/goksel/Sites/test
There are 2 options available. If you right-click on the project you can add an external builder, which can be an ant file or a program. That will run on every file change.
The second option is to use something like Remote System Explorer from Target Management: http://www.eclipse.org/tm/ A lot of users use this when working on projects (like PHP) that they want synced up to a remote system.