Different software can yield varied results for 3D damped spring plots due to differences in their algorithms and underlying physics models. The user compared outputs from Maxima's gnuplot engine and WolframAlpha, noting discrepancies in the results. The accuracy of each software depends on the specific parameters and settings used during the simulation. Users are encouraged to verify the input conditions and review the documentation for each software to understand potential sources of error. Ultimately, the choice of software may impact the reliability of the results for damped spring simulations.