I recently reached the Twitter limit to add new followees so I’ve wrote a tiny Python script, Twitter Cleaner, to remove people who haven’t send anything for a number of days (30 by default) – and consequently be able to add new ones. It’s now available on github.
Note that it might conflict with the previous Twitter TOS if you unfollow too many people at once. However, it will happen only once if you put it into a daily crontab. It was safe in my case, but I can’t guarantee it will be in yours. You may also reach the API rate-limiting if you’ve too many followees.
It’t built using python-twitter, and is available under the MIT license.