Hrm, if some games use DosBox, can us Linux folks replace the GOG DoxBox with the Linux version? I hope my question makes sense. :)
What I do is installing the game using the GOG.com installer with wine. Then I copy the game directory to somewhere on /home and deinstall the game. Then I run the Linux native version of Dosbox to play the game.
I do take a peek at how GOG.com has modified the dosbox.conf and sometimes I adjust my own dosbox.conf if the game runs sloppy.