Recently after installing a fresh copy of Eclipse 3.4 on my PC, I ran into an issue with the "Open Resouce" dialog ([CTRL]+[SHIFT]+[R]) where it was showing all my SVN files. Installing Subclipse is supposed to make the Eclipse IDE automatically hide the .svn-base files from showing up (via the "Team" interface) but it wasn't working out for me.
Turns out there was a very easy solution to this problem—just right click on the project and choose "Close Project" from the menu. After the project closes, just right-click on the project and select "Open Project." This should reinitialize all the settings on a project and appears to registered the handling of automatically hiding the .svn-base files.
An alternative, would be to add the find your org.eclipse.ui.ide_3.4.*.jar (org.eclipse.ui.ide_3.4.2.M20090127-1700.jar) and then modify the plugin.xml file to include the filter "*.svn-base". I don't like this option because it requires you to change a JAR that could later be updated.
If you choose that route, close Eclipse and open the JAR with a Zip extraction tool. Next, search the plugin.xml for the text "<filter". There should be one filter tag: