Ikiwiki has already been optimised a lot, however..
Don't render blog archive pages unless a page is added/removed. Just changing a page doesn't affect the archives as they show only the title.
Look at splitting up CGI.pm. But note that too much splitting can slow perl down.
The backlinks calculation code is still O(N^2) on the number of pages. If backlinks info were stored in the index file, it would go down to constant time for iterative builds, though still N^2 for rebuilds.