SAGA GIS allows you to edit pixel values in a raster, one at a time. This is very useful for some purposes, e.g. remote sensing where you might what to select a specific pixel for spectral analysis. If you select the grid that you want to edit in the 'manager' panel, select the 'attributes' tab in the properties panel, and you can select a single pixel, or drag and select a block of pixels on screen, and then type in their values into the matrix that will be displayed under the attributes.
An option modify one pixel at a time with QGIS is to use the experimental plugin Serval to set a different value to a specific pixel.
