Try the following:
Project > Properties > Resource > Resource Filters > Add
Select: Exclude All, Folders, All Children (recursive)
Name Matches: .svn
OK and Apply
What if the plugin isn't doing the work for you? Like in my situation, I have subclipse installed, but it's not hidding the files! I even uninstalled-reinstalled
Nevermind, this blog post solved the issue: http://blog.pengoworks.com/index.cfm/2009/4/20/Eclipse-showing-svnbase-files-in-Open-Resource-dialog
The Subversive/Subclipse installer will do everything for you (ignore .svn as resource), plus you get SVN support...
If you can not, for some reason, install a SVN plugin as suggested by gimpf, you can filter the list of the Open Resource dialog.
As indicated in this SO question, you have at the top-right corner of the "Open Resource" dialog box a small blue arrow.
Click it and "Select Working Set".
Then create a new working set as required to include only what you need.
alt text http://giano.com.dist.unige.it/eclipseMirror/eclipse/downloads/drops/R-3.3-200706251500/whatsnew/images/openresource.png
Not as practical as having a plugin do the work for you though ;)
As Doug indirectly pointed out, you must close and reopen the project in Eclipse after installing Subversive or Subclipse.
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