On Fourth Street next to the Courthouse Square, there's a Cold Stone store -- the much-touted new chain that's the Benihana of ice cream. At Cold Stone you choose a flavor of ice cream and whatever additions you fancy (fruit, chocolate chips, nuts, etc.), and they mix it for you with paddles on a marble slab.
It's very showy but incredibly expensive: $3.09 for the equivalent of a single scoop (and one free addition) in a cup. A cone and extra additions cost more, so you could theoretically end up with a $7 ice cream cone.
The ice cream is only okay, nothing special; you could get the same quality from the dairy case at 7 Eleven.
Unique Suggestions: 1) Skip the coconut, which tastes like shredded styrofoam.
2) Remind yourself that you're on vacation, when even overrated, overpriced experiences are entertaining.
3) Walk around the corner, up A Street to 5th Avenue. There's a tiny park with benches next to the parking garage where you can sit in the shade and consume your $7 cone. Then go across the street to Mission San Rafael and visit the chapel and museum.