I strongly advise against messing with the backup utility/etc methods; the backup doesn't backup everything so if you erase certain DRM stuff you can't get it back (transfer utility seems to be the only magic way to do this). I would avoid messing with the restore tool at all unless you've actually lost your data.
There is now a way to easily delete all or most or multiple save files on a more recent version of the PS3 software.
Go into Saved Data Utility, then press square until you see "group by title", you'll see folders for each game. Go to a game with a large number of save files and press triangle on any one save file. Check "Sort By" and make sure it's sorted by "update date v", then go to Multiple in the menu. You'll see a list of checkboxes.
You can pick and choose which files to remove, or in the case of a very large set of files, pick "select all" to mark all of them for deletion, then uncheck (press X) specific data you want to keep. If you sorted the items properly above, the top files should be your most recent ones.
Select OK to delete all checked files. Repeat for all games you want to do this for; you should only need to do it for games with very large numbers of save files (many games don't let you make more than one or store multiple saves in one "file").