[eluser]TheFuzzy0ne[/eluser]
Judging by the allowed URI characters, I think urlencode() and urldecode() would work great. It's as if CodeIgniter was built with this problem in mind. It would also mean that search pages can be bookmarked, as with codeigniter.com's current system, the MD5 hash is removed from the database after a few hours, so any bookmarks to search results are rendered useless.
Thanks again to you both for your input.