Where I normally start with after a clean checkout from CI is our in-house Auth library (just because I know it by hearth), usually 3 base controllers to replace MY_Controller (front-end, back-end, admin), some custom helpers (data sanitation, date/time) I have gotten used to, an MY_Model based on this and our in-house MY_Router to have some extra routing ‘magic’.
Other than that it’s pretty much a basic install: usually I just extend some core feature to suit my personal preference, which is imho one of the greatest strengths of CodeIgniter in general.