Scratch

Do you mean save a project as in saving your progress at a checkpoint in a game, ot save a project as in make it so you can exit Scratch, come back and work on it more? Please be specific.

Well, if the game was one mode/one character, you could make a variable called 'savegame' or something. Set it to 0 before uploading it, but don't make a 'when start clicked, set it to 0' script. Whenever the character touches a specific check point, you could change the variable to whatever, but it has to be checkpoint-specific. For example, you could do something like 'checkpoint1' for the first one, 'checkpoint2' for the second, and so on.
Then, you could make an option on the title screen called 'load game.' When you clicked on that option, do 'if savegame=checkpoint1' go to the first checkpoint, 'if savegame=checkpoint2' go to the second one, and so on.

Hope this helped!