eggs, copley fountain, and the charles river benches are good spots, though depending on when you go it can be a pretty bad bust. eggs is right across from north station on the green line, or a skate down the street from north station on the orange line, copley is right down the street from back bay station on the orange line, the charles river benches are right near the charles mgh stop on the red line. you can also take the red line into harvard and find some sick stuff, like the jfk monument. you can pretty much take the train wherever and find something sick/fun.
there is orchard in roxbury, true east in downtown crossing, concepts near harvard square, and coliseum right off the last stop on the orange line in melrose as far as shops go
as for food, i tend to just got to either stop'n'stop or wild oats to get something to eat, but i know the penguin is good and it is right down the street from orchard