Channel estimation is of great importance in many wireless communication systems, since it influences the overall performance of a system significantly. Especially in multi-user and/or multi-antenna systems, i.e. generally in multi-branch systems, the requirements on channel estimation are very high, since the training signals or so called pilots that are used for channel estimation suffer from multiple access interference. Recently, in the context with such systems more and more attention is paid to concepts for joint channel estimation (JCE) which have the capability to eliminate the multiple access interference and also the interference between the channel coefficients. The performance of JCE can be evaluated in noise limited systems by the SNR degradation and in interference limited systems by the variation coefficient. Theoretical analysis carried out in this thesis verifies that both performance criteria are closely related to the patterns of the pilots used for JCE, no matter the signals are represented in the time domain or in the frequency domain. Optimum pilots like disjoint pilots, Walsh code based pilots or CAZAC code based pilots, whose constructions are described in this thesis, do not show any SNR degradation when being applied to multi-branch systems. It is shown that optimum pilots constructed in the time domain become optimum pilots in the frequency domain after a discrete Fourier transformation. Correspondingly, optimum pilots in the frequency domain become optimum pilots in the time domain after an inverse discrete Fourier transformation. However, even for optimum pilots different variation coefficients are obtained in interference limited systems. Furthermore, especially for OFDM-based transmission schemes the peak-to-average power ratio (PAPR) of the transmit signal is an important decision criteria for choosing the most suitable pilots. CAZAC code based pilots are the only pilots among the regarded pilot constructions that result in a PAPR of 0 dB for the transmit signal that origins in the transmitted pilots. When summarizing the analysis regarding the SNR degradation, the variation coefficient and the PAPR with respect to one single service area and considering the impact due to interference from other adjacent service areas that occur due to a certain choice of the pilots, one can conclude that CAZAC codes are the most suitable pilots for the application in JCE of multi-carrier multi-branch systems, especially in the case if CAZAC codes that origin in different mother codes are assigned to different adjacent service areas. The theoretical results of the thesis are verified by simulation results. The choice of the parameters for the frequency domain or time domain JCE is oriented towards the evaluated implementation complexity. According to the chosen parameterization of the regarded OFDM-based and FMT-based systems it is shown that a frequency domain JCE is the best choice for OFDM and a time domain JCE is the best choice for FMT applying CAZAC codes as pilots. The results of this thesis can be used as a basis for further theoretical research and also for future JCE implementation in wireless systems.