Considering the widespread use of effective capacity in cross-layer design and the extensive existence of renewal service processes in communication networks, this paper thoroughly investigates the effective capacity for renewal processes. Exact expressions of the effective capacity at a given quality of service (QoS) exponent are derived for the renewal processes with either constant or variable reward. The simple expressions reveal meaningful insights, such as the monotonicity and bounds of the effective capacity. The analytical results are then applied to evaluate the cross-layer throughput for diverse hybrid automatic repeat request (HARQ) systems, including fixed-rate HARQ (FR-HARQ, e.g., Type I HARQ, HARQ with chase combining (HARQ-CC) and HARQ with incremental redundancy (HARQ-IR)), variable-rate HARQ (VR-HARQ) and cross-packet HARQ (XP-HARQ). Furthermore, aiming at maximizing the effective capacity via the optimal rate selection, it is disclosed that VR-HARQ and XP-HARQ attain almost the same performance, and both of them perform better than FR-HARQ. In contrast, most of the prior outcomes approximate the effective capacity with the lack of insightful discussions that hampers the optimal design of HARQ systems. Finally, numerical results corroborate the analytical ones.