Since identi.ca has introduced support for the Twitter API, switching Twitterrific over seems to be as easy as entering this command in a Terminal window:
defaults write com.iconfactory.Twitterrific baseUrl -string 'identi.ca/api'
The command to switch back is the following:
defaults write com.iconfactory.Twitterrific baseUrl -string 'twitter.com'
You'll also need to restart Twitterrific after each of these to see the change working.
It took me awhile to figure this out, because I didn't realize that they'd hidden the details in plain sight. You know, like, in the README file that comes with the Twitterrific download. Sheesh. Who reads those?