Automatic EOL conversion in Eclipse
In addition to the Window > Preferences > General > Workspace setting for new files that you already know about, there is a File > Convert Line Delimiters To option. I don't know of any existing plugin/tool that will do this automatically when you save, but you could certainly write one or make converting the line ending part of your process.
To make it easier on yourself, you can bind keyboard shortcuts to the conversion commands by going to Window > Preferences > General > Keys and filtering using "delimiter":
You can Search your resources with the Search-Dialog and go to the tab File Search. There you can enter a Regular expression. Enter \r\n or whatever line ending you want to change.
Then hit the Replace .. Button instead of Search.
I want just setup once and be sure that all line endings are in the same format.
... ok, my answer does not consider this.
You might get usefull results with Eclipse save actions: If the eclipse formatter also converts the EOL style, you could use it to modify EOL style only for the files you are modifying.
Unfortunately I don't have eclipse here, so I can't test if this actually works. Worth a try, however.
In Eclipse, to convert the line endings for existing files:
Go to the file browser view, and click on the project/folder/file that you wish to convert.
From the menu bar, select File > Convert Line Delimiters To > Windows / Unix / MacOS 9.
