Large-scale multiple-input and multiple-output (MIMO) systems are capable of achieving high date rate. However, given the high hardware cost and excessive power consumption of massive MIMO systems, as a remedy, intelligent metasurfaces have been designed for efficient holographic MIMO (HMIMO) systems. In this paper, we propose a HMIMO architecture based on stacked intelligent metasurfaces (SIM) for the uplink of cell-free systems, where the SIM is employed at the access points (APs) for improving the spectral- and energy-efficiency. Specifically, we conceive distributed beamforming for SIM-assisted cell-free networks, where both the SIM coefficients and the local receiver combiner vectors of each AP are optimized based on the local channel state information (CSI) for the local detection of each user equipment (UE) information. Afterward, the central processing unit (CPU) fuses the local detections gleaned from all APs to detect the aggregate multi-user signal. Specifically, to design the SIM coefficients and the combining vectors of the APs, a low-complexity layer-by-layer iterative optimization algorithm is proposed for maximizing the equivalent gain of the channel spanning from the UEs to the APs. At the CPU, the weight vector used for combining the local detections from all APs is designed based on the minimum mean square error (MMSE) criterion, where the hardware impairments (HWIs) are also taken into consideration based on their statistics. The simulation results show that the SIM-based HMIMO outperforms the conventional single-layer HMIMO in terms of the achievable rate. We demonstrate that both the HWI of the radio frequency (RF) chains at the APs and the UEs limit the achievable rate in the high signal-to-noise-ratio (SNR) region.