Low-density parity-check (LDPC) codes have attracted much attention over the past two decades since they can asymptotically approach the Shannon capacity in a variety of data transmission and storage scenarios. As a type of promising structured LDPC codes, the protograph LDPC codes not only inherit the advantage of conventional LDPC codes, i.e., excellent error performance, but also possess simple representations to realize fast encoding and efficient decoding. This paper provides a comprehensive survey on the state-of-the-art in protograph LDPC code design and analysis for different channel conditions, including the additive white Gaussian noise (AWGN) channels, fading channels, partial response (PR) channels, and Poisson pulse-position modulation (PPM) channels. Moreover, the applications of protograph LDPC codes to joint source-and-channel coding (JSCC) and joint channel-and-physical-layer-network coding (JCPNC) are reviewed and studied. In particular, we focus our attention on the encoding design and assume the decoder is implemented by the belief propagation (BP) algorithm. Hopefully, this survey may facilitate research in this area.