Are there any methodologies and references to measure effectiveness of information systems application and information in an higher learning organization?
Can we implement COBIT or ITIL in an educational institution?
I guess this depends on your definition of effectiveness. If you want to measure whether users accept the information system, you could use the Technology Acceptance Model (Davis, 1989). If you want to measure whether the information system is used, you can use the Unifed Theory of Acceptance and Use of Technology (UTAUT; Venkatesh et al. 2003). If you want to measure whether the system achieves some desired outcomes, you could use the Information System Success Model (DeLone & McLean, 1992, 2003).
The Association for Information Systems lists a whole bunch of theories to measure IS 'effectiveness' in some form (http://istheory.byu.edu/wiki/Main_Page).
As Shareef et al. (2011) have shown effectiveness (and adoption) of IS is dependent on the application area. Be mindful, which problem you want to tackle with your IS and study the environment accordingly.
I actually teach my students not to reside on computer science or IT but get a deep knowledge of the fields they want to apply ICT.