In this paper, first, a broad overview of existing covert channel communication-based security attacks is provided. Such covert channels establish a communication link between two entities that are not authorized to share data. The secret data is encoded into different forms of signals, such as delay, temperature, or hard drive location. These signals and information are then decoded by the receiver to retrieve the secret data, thereby mitigating some of the existing security measures. The important steps of covert channel attacks are described, such as data encoding, communication protocol, data decoding, and models to estimate communication bandwidth and bit error rate. Countermeasures against covert channels and existing covert channel detection techniques are also summarized. In the second part of the paper, the implications of such attacks for emerging packaging technologies, such as 2.5D/3D integration are discussed. Several covert channel threat models for 2.5D/3D ICs are also proposed.