Although Sam and Max spend a lot of time in their office or traipsing around the world, they have a house in a suburb outside New York city. Its been seen in the comics and animated series. Currently, the only rooms seen/mentioned are the kitchen, living room, dining room, and bedroom, all filled with all sorts of odd objects and trash.
The kitchen was first seen in the comic The Damned Don't Dance where Sam was "cooking" Christmas dinner. In Sam and Max's letter to the fans ("Sam & Max's 1994 Holiday Newsletter"), Sam strapped Max to the kitchen table in order to pull out "a suspicious growth behind one of his fluffy ears".
The living room and dining room were also seen in The Damned Don't Dance. In the animated series, the living room has a couch, TV, and an impressionistic painting of Sam and Max in a rowboat at night (a reference to a famous painting, no doubt). Sam and Max's bedroom always has a bunk bed and they apparently switch bunks whenever they feel like it.