This paper aims to handle the joint transmitter and noncoherent receiver design for multiuser multiple-input multiple-output (MU-MIMO) systems through deep learning. Given the deep neural network (DNN) based noncoherent receiver, the novelty of this work mainly lies in the multiuser waveform design at the transmitter side. According to the signal format, the proposed deep learning solutions can be divided into two groups. One group is called pilot-aided waveform, where the information-bearing symbols are time-multiplexed with the pilot symbols. The other is called learning-based waveform, where the multiuser waveform is partially or even completely designed by deep learning algorithms. Specifically, if the information-bearing symbols are directly embedded in the waveform, it is called systematic waveform. Otherwise, it is called non-systematic waveform, where no artificial design is involved. Simulation results show that the pilot-aided waveform design outperforms the conventional zero forcing receiver with least squares (LS) channel estimation on small-size MU-MIMO systems. By exploiting the time-domain degrees of freedom (DoF), the learning-based waveform design further improves the detection performance by at least 5 dB at high signal-to-noise ratio (SNR) range. Moreover, it is found that the traditional weight initialization method might cause a training imbalance among different users in the learning-based waveform design. To tackle this issue, a novel weight initialization method is proposed which provides a balanced convergence performance with no complexity penalty.