Some of the larger sets are getting posted at Pleasuredome with all the naming set according to the HS databases.
I've been renaming some of my sets recently and I've found that XYplorer's mass renaming functions can be quite handy. Probably saved hours using search/replace to fix region codes and regex to remove all the TOSEC disc ids. A little more is needed here and there but that cuts out a lot of the work. I haven't messed with cue files yet, but http://www.hyperspin-fe.com/forum/showthread.php?22533-Yet-another-feature-rich-Hyperspin-rom-amp-media-manager should be able to fix 'em all once everything is named correctly.