According to Donncha O Caoimh a new version of WP Super Cache is available.

This release addresses some issues large or busy sites had with deleting expired cache files. Some sites generated so many cache files that there were two [sic] many files generated, even when those files were cleared out every hour. To fix that I limited the recursive function that deletes the files to 100 deletions at a time. That function is called until all the cache files are deleted (or strictly speaking, no files are deleted. That’s how the expired file cleanup works).
It’s also possible to set the garbage collection interval to 10 minutes now which will also help.

This is one of those plugins I continually tell people with WordPress blogs that are interesting, (because they get a lot more visitors than I do) to get. If you use WordPress you should use this plugin.