Here are the files, which don't have eol-style = native:
M wp-includes/js/jquery/jquery.color.js
M wp-includes/js/jquery/jquery.js
M wp-includes/js/jquery/jquery.form.js
M wp-includes/js/scriptaculous/wp-scriptaculous.js
M wp-includes/js/scriptaculous/prototype.js
M wp-includes/js/scriptaculous/builder.js
M wp-includes/js/scriptaculous/sound.js
M wp-includes/js/scriptaculous/MIT-LICENSE
M wp-includes/js/scriptaculous/effects.js
M wp-includes/js/scriptaculous/unittest.js
M wp-includes/js/scriptaculous/scriptaculous.js
M wp-includes/js/scriptaculous/dragdrop.js
M wp-includes/js/scriptaculous/slider.js
M wp-includes/js/scriptaculous/controls.js
M wp-includes/js/crop/cropper.css
M wp-includes/js/tinymce/license.txt
M wp-includes/js/tinymce/plugins/autosave/readme.txt
M wp-includes/js/tinymce/langs/wp-langs.php
M wp-content/themes/default/rtl.css
M wp-config-sample.php
M wp-admin/includes/dashboard.php
M wp-admin/js/custom-fields.js
M wp-admin/js/categories.js
M wp-admin/js/users.js
M wp-admin/css/widgets-rtl.css
Of these, wp-config-sample.php (which already is), wp-includes/js/tinymce/license.txt, wp-includes/js/tinymce/plugins/autosave/readme.txt, wp-includes/js/scriptaculous/MIT-LICENSE whould stay CLRF, because there is a chance they will be abused by notepaders.
Also, there are few more files, which should be CLRF-ed: license.txt and wp-includes/images/crystal/license.txt.
This process could be turned into a routine:
cd /path/to/wp/clean/trunk
EXCLUDES="license.txt wp-config-sample.php wp-includes/js/tinymce/license.txt wp-includes/js/tinymce/plugins/autosave/readme.txt wp-includes/js/scriptaculous/MIT-LICENSE license.txt wp-includes/images/crystal/license.txt"
svn propset -R svn:eol-style native *
for f in $EXCLUDES; do svn revert $f; done