To be honest, Sam and Max works better when it doesn't get a chance to build up a big continuity. By the end of Season 3 I didn't know if they were mocking the idea of having too much continuity, or actively trying to retcon some events to make it all work together, but either way it felt like it had drawn on too long.
That's not to say that I don't want Sam and Max. But I like how I can read the comics, then go to the cartoon show, then go to the Lucas Arts game, then go to the Telltale Games and each time get an experience which is recognizably Sam and Max, but a different take on things with most of the characters different. I'm sure eventually they'll show up again in some other form.