http://www.finebytes.com/mfr/ Magic File Renamer
You can right click a directory, sort all the files by creation date, last write date and things like that. Then choose and name and tell it to automatically add a counter.
name-001.jpg
name-002.jpg
name-003.jpg
...
You can also grab the subdirectories in directories and have it do them as well. It's good.