I had the same problem, it went on until I had 44G of InnoDB space, with only 4G free. After getting tired of having to increase the number of files every week, I decided to dump all data with mysqldump, remove the files+ logs and recreate them. After that there was more than 24G free, and the database was a bit faster too :) (it took me more than 12 hours to dump & restore, but it was worth the effort).

In your case I think you should do the same only if you are running out of space every week or something. I too noticed that innodb won't give up it space, so this was the only solution that came to my mind, maybe there is a better way, but i haven't seen any tools to defragment an innodb database.