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Depending on your setup, you can currently have each student save to their own directory, if they have their own network folder (e.g., an "H:" drive on Windows, that maps to a different networked folder for each student).

Alternatively, you can try the wrapper program, located here: ftp://ftp.tuxpaint.org/unix/x/tuxpaint/savedir/

In the meantime, we are working on OS file dialog support as part of the 2008 Google Summer of Code program, and the request to add file dialogs are documented elsewhere in the SF.net Features Request database (#1455978) so closing this request as a dup. Thanks!