[eluser]bretticus[/eluser]
[quote author="kurucu" date="1252350629"]PHP sessions would not delete custom files or rows in the database, only session data just like CodeIgniter.[/quote]
Yeah, that was meant as an example for the model, not a suggestion. Hope I didn't confuse you there. I was just trying to say that even PHP sessions have to use the model of garbage collection because of HTTP being stateless. That's why I recommended a script that is evoked from cron. The script, of course, needs to be able to run a database query just like your PHP scripts. If your database information that needs garbage collection has a timestamp of some kind then this is possible (because your query can check for records that are stale: not updated since...)
Sounds like it's not session data though that you need to clean up since you had session handling in a cookie separate from the data. However, it might not be a bad idea to incorporate that data into CI session database mode. Then CI will clean it up for you automatically.