Workaround for managing individual custom labels in Eclipse Force.com IDE
Unfortunately the Force.com IDE does not yet support individual custom label selection even though the UI does. There is a bug/issue filled so please upvote it at this link Selection of individual `CustomLabels` not working There is a workaround however.
One must manually update the `package.xml` and specify the metadata member `CustomLabel` (no s at the end) and the individual labels like so. Also ensure you don't have the labels node selected through the Eclipse Force.com IDE UI, that is there should not be an entry in your `package.xml` for member `CustomLabels`. One annoying caveat of this is to edit `CustomeLabels.labels` you must be in offline ('Right click root project > Force.com > Work Offline') mode otherwise it get's still refreshed from the server.
<types> <members>Label_1</members> <members>Label_2</members> <members>...</members> <name>CustomLabel</name> </types>
If this has helped you feel free to comment or follow me on twitter @danielsoklows.