DigitizeIt can automatically digitize scatter-plots. Results may vary depending on the quality and colors of your graph.
To automatically digitize a scatter-plot, select Auto->Find Symbols. Now click on one of the symbols, that you want to digitize. It is important to click on a part of the symbol, that has a color different from the background color of your graph, e.g. if you want to digitize circles with a black border but filled with the background color, click on the black border. The size and center of the symbol are then detected automatically and DigitizeIt will find all similar symbols within the entire graph and put them into a new data set. If you have defined a search region only symbols within the search region are detected.
If DigitizeIt did not find all of the symbols or too many, you need to adjust the color and similarity settings in the Auto Options dialog.