One of the key challenges for future communication systems is to deal with fast changing channels due to the mobility of users. Having a robust protocol capable of handling transmission failures in unfavorable channel conditions is crucial, but the feedback capacity may be greatly limited due to strict latency requirements. This paper studies the hybrid automatic repeat request (HARQ) techniques involved in re-transmissions when decoding failures occur at the receiver and proposes a scheme that relies on codeword bundling and adaptive incremental redundancy (IR) to maximize the overall throughput in a limited feedback system. In addition to the traditional codeword extension IR bits, this paper introduces a new type of IR, bundle parity bits, obtained from an erasure code across all the codewords in a bundle. The type and number of IR bits to be sent as a response to a decoding failure is optimized through a Markov Decision Process. In addition to the single link analysis, the paper studies how the same techniques generalize to relay and multi-user broadcast systems. Simulation results show that the proposed schemes can provide a significant increase in throughput over traditional HARQ techniques.