PSI-Plot and ProStat support 3D-scatter plots and 3D error bar plots. A 3D plot can be rotated and resized in 3 directions. The background can be turned on/off. You can also add on projection curves to any of the three planes.
3D scatter plot
Without perspective
With projection in X-plane
Projection in Z-plane plus drop lines
Error bar chart
Error bar chart at different angles