Over the last years, international sea-freight container transportation has grown dramatically and container terminals play nowadays a key-role in the global shipping network. The increased competitiveness among terminals requires more and more efficiency in container operations, both along the quayside and within the yard, in order to minimize ships turnaround time. Operations research methods and techniques are therefore worth being used in optimizing terminal operations. In this work, we first give an overview of decision problems which arise in the management of a container terminal (e.g. berth allocation, crane scheduling, storage policies and strategies, transfer operations) and we briefly describe models and methods presented in the literature. Then, starting from a collaboration with some of the busiest ports in Europe, we have identified some critical issues which will be illustrated: in particular, we focus on the impact that gate operations and transshipment operations have on the yard and we propose a new approach to the yard management which takes into account these interactions. We conclude with suggestions of possible research tracks and open issues.