Internet of Things (IoT) is a disruptive technology with applications across diverse domains such as transportation and logistics systems, smart grids, smart homes, connected vehicles, and smart cities. Alongside the growth of these infrastructures, the volume and variety of attacks on these infrastructures has increased highlighting the significance of distinct protection mechanisms. Intrusion detection is one of the distinguished protection mechanisms with notable recent efforts made to establish effective intrusion detection for IoT and IoV. However, unique characteristics of such infrastructures including battery power, bandwidth and processors overheads, and the network dynamics can influence the operation of an intrusion detection system. This paper presents a comprehensive study of existing intrusion detection systems for IoT systems including emerging systems such as Internet of Vehicles (IoV). The paper analyzes existing systems in three aspects: computational overhead, energy consumption and privacy implications. Based on a rigorous analysis of the existing intrusion detection approaches, the paper also identifies open challenges for an effective and collaborative design of intrusion detection system for resource-constrained IoT system in general and its applications such as IoV. These efforts are envisaged to highlight state of the art with respect to intrusion detection for IoT and open challenges requiring specific efforts to achieve efficient intrusion detection within these systems.