Recently, hybrid-automatic-repeat-request (HARQ) systems have been favored in particular state-of-the-art communications systems since they provide the practicality of error detections and corrections aligned with repeat-requests when needed at receivers. The queueing characteristics of these systems have taken considerable focus since the current technology demands data transmissions with a minimum delay provisioning. In this paper, we investigate the effects of physical layer characteristics on data link layer performance in a general class of HARQ systems. Constructing a state transition model that combines queue activity at a transmitter and decoding efficiency at a receiver, we identify the probability of clearing the queue at the transmitter and the packet-loss probability at the receiver. We determine the effective capacity that yields the maximum feasible data arrival rate at the queue under quality-of-service constraints. In addition, we put forward non-asymptotic backlog and delay bounds. Finally, regarding three different HARQ protocols, namely Type-I HARQ, HARQ-chase combining (HARQ-CC) and HARQ-incremental redundancy (HARQ-IR), we show the superiority of HARQ-IR in delay robustness over the others. However, we further observe that the performance gap between HARQ-CC and HARQ-IR is quite negligible in certain cases. The novelty of our paper is a general cross-layer analysis of these systems, considering encoding/decoding in the physical layer and delay aspects in the data-link layer.